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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376621	XR_931176.3	n.91-2181T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308500	ENST00000834606.1	n.91-2181T>C		intron_variant	Intron 1 of 3
ENSG00000308500	ENST00000834607.1	n.136-2181T>C		intron_variant	Intron 1 of 3
ENSG00000308500	ENST00000834608.1	n.92-2181T>C		intron_variant	Intron 1 of 3

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 v4.3

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;