rs7144649

Variant names:

• chr14-57355498-G-A
• rs7144649
• ENST00000556602.1:n.53G>A

Variant summary

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

The ENST00000556602.1(ENSG00000259008):​n.53G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 152,062 control chromosomes in the GnomAD database, including 32,434 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 0.60 (32433 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: ENSG00000259008 ENST00000556602.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 13 publications found

Genes affected

ENSG00000259008 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556602.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259008	ENST00000556602.1	TSL:6	n.53G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000286355	ENST00000720319.1		n.119-2277C>T		intron	N/A
	ENSG00000286355	ENST00000720320.1		n.118-2277C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91625 AN: 151942 Hom.: 32449 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.634

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.602 AC: 91607 AN: 152060 Hom.: 32433 Cov.: 32 AF XY: 0.607 AC XY: 45127 AN XY: 74326

African (AFR) AF: 0.204 AC: 8446 AN: 41444

American (AMR) AF: 0.673 AC: 10283 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2290 AN: 3472

East Asian (EAS) AF: 0.758 AC: 3918 AN: 5170

South Asian (SAS) AF: 0.614 AC: 2954 AN: 4812

European-Finnish (FIN) AF: 0.831 AC: 8800 AN: 10594

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52595 AN: 67976

Other (OTH) AF: 0.632 AC: 1331 AN: 2106

Alfa AF: 0.706 Hom.: 127385

Bravo AF: 0.574

Asia WGS AF: 0.628 AC: 2188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.8
DANN	Benign	0.67
PhyloP100		1.1

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: rs7144649;

hg19: chr14-57822216;