rs7941248

Variant names:

• chr11-33904428-T-C
• rs7941248
• ENST00000834606.1:n.91-2181T>C

Variant summary

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

The ENST00000834606.1(ENSG00000308500):​n.91-2181T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 151,858 control chromosomes in the GnomAD database, including 38,293 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 0.71 (38293 hom., cov: 29)
• Consequence: ENSG00000308500 ENST00000834606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 7 publications found

Genes affected

ENSG00000308500 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000834606.1. 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
	ENSG00000308500	ENST00000834606.1		n.91-2181T>C		intron	N/A
	ENSG00000308500	ENST00000834607.1		n.136-2181T>C		intron	N/A
	ENSG00000308500	ENST00000834608.1		n.92-2181T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107036 AN: 151742 Hom.: 38259 Cov.: 29

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.705 AC: 107117 AN: 151858 Hom.: 38293 Cov.: 29 AF XY: 0.701 AC XY: 52006 AN XY: 74186

African (AFR) AF: 0.770 AC: 31886 AN: 41418

American (AMR) AF: 0.605 AC: 9225 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2160 AN: 3472

East Asian (EAS) AF: 0.502 AC: 2591 AN: 5158

South Asian (SAS) AF: 0.624 AC: 2993 AN: 4800

European-Finnish (FIN) AF: 0.759 AC: 8005 AN: 10546

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.707 AC: 47990 AN: 67914

Other (OTH) AF: 0.666 AC: 1404 AN: 2108

Alfa AF: 0.700 Hom.: 158158

Bravo AF: 0.698

Asia WGS AF: 0.524 AC: 1823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.39
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs7941248; hg19: chr11-33925975;