rs7629386

Variant names:

• chr3-40925416-C-T
• rs7629386
• ENST00000726235.1:n.773+14342C>T

Variant summary

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

The ENST00000726235.1(ENSG00000294831):​n.773+14342C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,072 control chromosomes in the GnomAD database, including 6,898 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 0.29 (6898 hom., cov: 32)
• Consequence: ENSG00000294831 ENST00000726235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 7 publications found

Genes affected

ENSG00000294831 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.328 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
ENSG00000294831	ENST00000726235.1	n.773+14342C>T		intron_variant	Intron 2 of 2
ENSG00000294831	ENST00000726236.1	n.348+14342C>T		intron_variant	Intron 3 of 3
ENSG00000294831	ENST00000726237.1	n.248+14342C>T		intron_variant	Intron 2 of 2
ENSG00000294831	ENST00000726238.1	n.244+14342C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44710 AN: 151954 Hom.: 6890 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.0588

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.294 AC: 44739 AN: 152072 Hom.: 6898 Cov.: 32 AF XY: 0.288 AC XY: 21381 AN XY: 74334

African (AFR) AF: 0.281 AC: 11655 AN: 41472

American (AMR) AF: 0.242 AC: 3701 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1186 AN: 3470

East Asian (EAS) AF: 0.0585 AC: 303 AN: 5176

South Asian (SAS) AF: 0.167 AC: 803 AN: 4818

European-Finnish (FIN) AF: 0.327 AC: 3453 AN: 10564

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22569 AN: 67970

Other (OTH) AF: 0.291 AC: 614 AN: 2112

Alfa AF: 0.313 Hom.: 29529

Bravo AF: 0.286

Asia WGS AF: 0.152 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.63
DANN	Benign	0.60
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs7629386; hg19: chr3-40966907;