rs9257691

Variant names:

• chr6-29301152-C-A
• rs9257691
• ENST00000733278.1:n.246-10600G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-29301152-C-A
• chr6-29301152-C-G
• chr6-29301152-C-T

Variant summary

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

The ENST00000733278.1(ENSG00000295863):​n.246-10600G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,952 control chromosomes in the GnomAD database, including 14,650 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 (14650 hom., cov: 32)
• Consequence: ENSG00000295863 ENST00000733278.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 7 publications found

Genes affected

ENSG00000295863 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000733278.1. 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
	ENSG00000295863	ENST00000733278.1		n.246-10600G>T		intron	N/A
	ENSG00000295863	ENST00000733279.1		n.390-10600G>T		intron	N/A
	ENSG00000295863	ENST00000733280.1		n.267-10600G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63669 AN: 151832 Hom.: 14638 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.419 AC: 63685 AN: 151952 Hom.: 14650 Cov.: 32 AF XY: 0.421 AC XY: 31281 AN XY: 74268

African (AFR) AF: 0.232 AC: 9636 AN: 41452

American (AMR) AF: 0.405 AC: 6180 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1444 AN: 3468

East Asian (EAS) AF: 0.325 AC: 1677 AN: 5166

South Asian (SAS) AF: 0.387 AC: 1864 AN: 4816

European-Finnish (FIN) AF: 0.593 AC: 6235 AN: 10522

Middle Eastern (MID) AF: 0.493 AC: 142 AN: 288

European-Non Finnish (NFE) AF: 0.519 AC: 35257 AN: 67944

Other (OTH) AF: 0.406 AC: 859 AN: 2114

Alfa AF: 0.416 Hom.: 13082

Bravo AF: 0.394

Asia WGS AF: 0.405 AC: 1407 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.059
DANN	Benign	0.28
PhyloP100		-0.42

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: rs9257691;

hg19: chr6-29268929;