rs6943360

Variant names:

• chr7-132020385-C-A
• rs6943360
• ENST00000774478.1:n.96+3114G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-132020385-C-A
• chr7-132020385-C-G
• chr7-132020385-C-T

Variant summary

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

The ENST00000774478.1(ENSG00000300842):​n.96+3114G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,058 control chromosomes in the GnomAD database, including 52,413 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 0.83 (52413 hom., cov: 31)
• Consequence: ENSG00000300842 ENST00000774478.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 1 publications found

Genes affected

ENSG00000300842 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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
ENSG00000300842	ENST00000774478.1	n.96+3114G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.829 AC: 125950 AN: 151940 Hom.: 52389 Cov.: 31

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.827

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

GnomAD4 genome AF: 0.829 AC: 126024 AN: 152058 Hom.: 52413 Cov.: 31 AF XY: 0.832 AC XY: 61805 AN XY: 74318

African (AFR) AF: 0.790 AC: 32748 AN: 41458

American (AMR) AF: 0.864 AC: 13197 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2766 AN: 3468

East Asian (EAS) AF: 0.983 AC: 5084 AN: 5170

South Asian (SAS) AF: 0.896 AC: 4317 AN: 4816

European-Finnish (FIN) AF: 0.847 AC: 8955 AN: 10572

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56281 AN: 67980

Other (OTH) AF: 0.830 AC: 1751 AN: 2110

Alfa AF: 0.826 Hom.: 82829

Bravo AF: 0.829

Asia WGS AF: 0.917 AC: 3186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.74
PhyloP100		-0.032

Splicing

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

Other links and lift over

dbSNP: rs6943360; hg19: chr7-131705144;