rs6935795

Variant names:

• chr6-21259097-G-T
• rs6935795
• ENST00000669568.2:n.296+11740C>A

Variant summary

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

The ENST00000669568.2(ENSG00000287404):​n.296+11740C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,048 control chromosomes in the GnomAD database, including 49,832 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 0.80 (49832 hom., cov: 31)
• Consequence: ENSG00000287404 ENST00000669568.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 4 publications found

Genes affected

ENSG00000287404 (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 (NFE) allele frequency at 95% confidence interval = 0.872 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
ENSG00000287404	ENST00000669568.2	n.296+11740C>A		intron_variant	Intron 1 of 3
ENSG00000287404	ENST00000724722.1	n.279+11740C>A		intron_variant	Intron 1 of 1
ENSG00000287404	ENST00000724723.1	n.123+11740C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122280 AN: 151928 Hom.: 49791 Cov.: 31

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.966

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.805 AC: 122378 AN: 152048 Hom.: 49832 Cov.: 31 AF XY: 0.803 AC XY: 59645 AN XY: 74316

African (AFR) AF: 0.682 AC: 28255 AN: 41418

American (AMR) AF: 0.766 AC: 11695 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2795 AN: 3472

East Asian (EAS) AF: 0.759 AC: 3908 AN: 5152

South Asian (SAS) AF: 0.795 AC: 3825 AN: 4812

European-Finnish (FIN) AF: 0.880 AC: 9321 AN: 10592

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.878 AC: 59719 AN: 68010

Other (OTH) AF: 0.822 AC: 1739 AN: 2116

Alfa AF: 0.852 Hom.: 234929

Bravo AF: 0.793

Asia WGS AF: 0.780 AC: 2710 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	0.18
DANN	Benign	0.34
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6935795; hg19: chr6-21259328;