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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839775.1. 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
	ENSG00000309240	ENST00000839775.1		n.78-1235C>T		intron	N/A
	ENSG00000309240	ENST00000839776.1		n.49-1235C>T		intron	N/A
	ENSG00000309240	ENST00000839777.1		n.49-1235C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs629681;

hg19: chr11-30761727;