chr14-35413729-A-T

Variant names:

• chr14-35413729-A-T
• rs2007960
• ENST00000848537.1:n.241+10342A>T

Variant summary

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

The ENST00000848537.1(ENSG00000310246):​n.241+10342A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 152,084 control chromosomes in the GnomAD database, including 29,840 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 0.62 (29840 hom., cov: 32)
• Consequence: ENSG00000310246 ENST00000848537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 9 publications found

Genes affected

ENSG00000310246 (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 (EAS) allele frequency at 95% confidence interval = 0.712 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
ENSG00000310246	ENST00000848537.1	n.241+10342A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94837 AN: 151966 Hom.: 29798 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.624 AC: 94930 AN: 152084 Hom.: 29840 Cov.: 32 AF XY: 0.630 AC XY: 46819 AN XY: 74356

African (AFR) AF: 0.581 AC: 24074 AN: 41464

American (AMR) AF: 0.708 AC: 10815 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2087 AN: 3460

East Asian (EAS) AF: 0.732 AC: 3787 AN: 5176

South Asian (SAS) AF: 0.718 AC: 3456 AN: 4816

European-Finnish (FIN) AF: 0.664 AC: 7024 AN: 10586

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41763 AN: 67984

Other (OTH) AF: 0.615 AC: 1296 AN: 2108

Alfa AF: 0.621 Hom.: 3654

Bravo AF: 0.625

Asia WGS AF: 0.752 AC: 2615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
DANN	Benign	0.48
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs2007960; hg19: chr14-35882935;