rs7931342

Variant names:

• chr11-69227030-T-G
• rs7931342
• ENST00000779509.1:n.139-21331T>G

Variant summary

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

The ENST00000779509.1(ENSG00000301530):​n.139-21331T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,944 control chromosomes in the GnomAD database, including 26,370 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 0.57 (26370 hom., cov: 32)
• Consequence: ENSG00000301530 ENST00000779509.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• Publications: 120 publications found

Genes affected

ENSG00000301530 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 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
ENSG00000301530	ENST00000779509.1	n.139-21331T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86374 AN: 151826 Hom.: 26326 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.569 AC: 86470 AN: 151944 Hom.: 26370 Cov.: 32 AF XY: 0.563 AC XY: 41829 AN XY: 74240

African (AFR) AF: 0.791 AC: 32783 AN: 41460

American (AMR) AF: 0.426 AC: 6497 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2323 AN: 3464

East Asian (EAS) AF: 0.218 AC: 1121 AN: 5150

South Asian (SAS) AF: 0.460 AC: 2218 AN: 4820

European-Finnish (FIN) AF: 0.479 AC: 5044 AN: 10528

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34701 AN: 67948

Other (OTH) AF: 0.574 AC: 1213 AN: 2112

Alfa AF: 0.526 Hom.: 87102

Bravo AF: 0.576

Asia WGS AF: 0.417 AC: 1448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.68
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs7931342; hg19: chr11-68994497;