14-42142757-A-G

Variant names:

• chr14-42142757-A-G
• rs7155941
• ENST00000836359.1:n.127-6813A>G

Variant summary

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

The ENST00000836359.1(ENSG00000308787):​n.127-6813A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 151,950 control chromosomes in the GnomAD database, including 41,387 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 0.74 (41387 hom., cov: 30)
• Consequence: ENSG00000308787 ENST00000836359.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 4 publications found

Genes affected

ENSG00000308787 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308787	ENST00000836359.1	n.127-6813A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112000 AN: 151830 Hom.: 41351 Cov.: 30

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.731

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.738 AC: 112096 AN: 151950 Hom.: 41387 Cov.: 30 AF XY: 0.741 AC XY: 55018 AN XY: 74272

African (AFR) AF: 0.738 AC: 30576 AN: 41408

American (AMR) AF: 0.739 AC: 11283 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2232 AN: 3468

East Asian (EAS) AF: 0.878 AC: 4526 AN: 5152

South Asian (SAS) AF: 0.736 AC: 3550 AN: 4824

European-Finnish (FIN) AF: 0.781 AC: 8236 AN: 10546

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.727 AC: 49402 AN: 67974

Other (OTH) AF: 0.735 AC: 1553 AN: 2114

Alfa AF: 0.730 Hom.: 17270

Bravo AF: 0.733

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.055
DANN	Benign	0.43
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7155941; hg19: chr14-42611960;