rs6943159

Variant names:

• chr7-11910435-C-A
• rs6943159
• ENST00000775347.1:n.291-3993G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-11910435-C-A
• chr7-11910435-C-G

Variant summary

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

The ENST00000775347.1(ENSG00000300984):​n.291-3993G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,924 control chromosomes in the GnomAD database, including 14,211 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 0.42 (14211 hom., cov: 32)
• Consequence: ENSG00000300984 ENST00000775347.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 0 publications found

Genes affected

ENSG00000300984 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775347.1. 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
	ENSG00000300984	ENST00000775347.1		n.291-3993G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63346 AN: 151808 Hom.: 14189 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.417 AC: 63427 AN: 151924 Hom.: 14211 Cov.: 32 AF XY: 0.420 AC XY: 31163 AN XY: 74270

African (AFR) AF: 0.536 AC: 22190 AN: 41432

American (AMR) AF: 0.447 AC: 6812 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1496 AN: 3470

East Asian (EAS) AF: 0.723 AC: 3724 AN: 5148

South Asian (SAS) AF: 0.389 AC: 1869 AN: 4810

European-Finnish (FIN) AF: 0.323 AC: 3418 AN: 10568

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22628 AN: 67928

Other (OTH) AF: 0.400 AC: 846 AN: 2114

Alfa AF: 0.368 Hom.: 34838

Bravo AF: 0.436

Asia WGS AF: 0.532 AC: 1848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.36
DANN	Benign	0.29
PhyloP100		-0.14

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: rs6943159;

hg19: chr7-11950061;