rs629681

Variant names:

• chr11-30740180-C-T
• rs629681
• ENST00000839775.1:n.78-1235C>T

Variant summary

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

The ENST00000839775.1(ENSG00000309240):​n.78-1235C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 151,852 control chromosomes in the GnomAD database, including 12,069 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 0.39 (12069 hom., cov: 33)
• Consequence: ENSG00000309240 ENST00000839775.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.555
• Publications: 3 publications found

Genes affected

ENSG00000309240 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928338	XR_007062640.1	n.78-1235C>T		intron_variant	Intron 1 of 4
LOC101928338	XR_242862.5	n.78-1235C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309240	ENST00000839775.1	n.78-1235C>T		intron_variant	Intron 1 of 4
ENSG00000309240	ENST00000839776.1	n.49-1235C>T		intron_variant	Intron 1 of 5
ENSG00000309240	ENST00000839777.1	n.49-1235C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59831 AN: 151732 Hom.: 12052 Cov.: 33

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.394 AC: 59892 AN: 151852 Hom.: 12069 Cov.: 33 AF XY: 0.394 AC XY: 29253 AN XY: 74196

African (AFR) AF: 0.339 AC: 14063 AN: 41460

American (AMR) AF: 0.347 AC: 5283 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1209 AN: 3460

East Asian (EAS) AF: 0.487 AC: 2494 AN: 5122

South Asian (SAS) AF: 0.537 AC: 2588 AN: 4820

European-Finnish (FIN) AF: 0.384 AC: 4047 AN: 10548

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28883 AN: 67898

Other (OTH) AF: 0.379 AC: 799 AN: 2108

Alfa AF: 0.424 Hom.: 7219

Bravo AF: 0.389

Asia WGS AF: 0.463 AC: 1611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.57
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs629681; hg19: chr11-30761727;