chr7-143477799-A-G

Variant names:

• chr7-143477799-A-G
• rs1404634
• ENST00000429289.5:n.207-26975A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000429289.5(EPHA1-AS1):​n.207-26975A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 1,443,876 control chromosomes in the GnomAD database, including 420,977 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.78 (46242 hom., cov: 29)
  • Exomes 𝑓: 0.76 (374735 hom.)
• Consequence: EPHA1-AS1 ENST00000429289.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 12 publications found

Genes affected

EPHA1-AS1 (HGNC:27799): (EPHA1 antisense RNA 1)

TAS2R41 (HGNC:18883): (taste 2 receptor member 41) This gene encodes a member of the bitter taste receptor family which belong to the G protein-coupled receptor superfamily and are predominantly expressed in taste receptor cells of the tongue and palate epithelia. This intronless taste receptor gene encodes a seven-transmembrane receptor protein, functioning as a bitter taste receptor. This gene is clustered together with eight other taste receptor genes on chromosome 7. Chloramphenicol is an agonist for the encoded protein. [provided by RefSeq, Jul 2017]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429289.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPHA1-AS1	NR_033897.1		n.207-26975A>G		intron	N/A
	TAS2R41	NM_176883.2	MANE Select	c.-74A>G		upstream_gene	N/A	NP_795364.2	P59536

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EPHA1-AS1	ENST00000429289.5	TSL:1	n.207-26975A>G		intron	N/A
	EPHA1-AS1	ENST00000690912.2		n.228-18167A>G		intron	N/A
	EPHA1-AS1	ENST00000703017.1		n.206-18167A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.777 AC: 117998 AN: 151844 Hom.: 46198 Cov.: 29

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.788

GnomAD4 exome AF: 0.761 AC: 982632 AN: 1291914 Hom.: 374735 AF XY: 0.759 AC XY: 490864 AN XY: 646898

African (AFR) AF: 0.854 AC: 25782 AN: 30202

American (AMR) AF: 0.735 AC: 31584 AN: 42950

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 17420 AN: 22892

East Asian (EAS) AF: 0.620 AC: 24015 AN: 38748

South Asian (SAS) AF: 0.709 AC: 54685 AN: 77182

European-Finnish (FIN) AF: 0.764 AC: 39148 AN: 51270

Middle Eastern (MID) AF: 0.752 AC: 3236 AN: 4304

European-Non Finnish (NFE) AF: 0.769 AC: 745609 AN: 970032

Other (OTH) AF: 0.757 AC: 41153 AN: 54334

GnomAD4 genome AF: 0.777 AC: 118102 AN: 151962 Hom.: 46242 Cov.: 29 AF XY: 0.774 AC XY: 57495 AN XY: 74258

African (AFR) AF: 0.847 AC: 35130 AN: 41460

American (AMR) AF: 0.748 AC: 11424 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 2622 AN: 3468

East Asian (EAS) AF: 0.622 AC: 3195 AN: 5134

South Asian (SAS) AF: 0.687 AC: 3297 AN: 4802

European-Finnish (FIN) AF: 0.772 AC: 8149 AN: 10558

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.764 AC: 51904 AN: 67954

Other (OTH) AF: 0.790 AC: 1665 AN: 2108

Alfa AF: 0.764 Hom.: 22966

Bravo AF: 0.780

Asia WGS AF: 0.692 AC: 2408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.74
PhyloP100		-0.051
PromoterAI		-0.0010	Neutral
Mutation Taster		=14/86	disease causing

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1404634;

hg19: chr7-143174892;

COSMIC: COSV68765264;