rs304256

Variant names:

• chr6-25050736-C-G
• rs304256
• ENST00000428903.1:n.79-4227C>G

Your query was ambiguous. Multiple possible variants found:

• chr6-25050736-C-G
• chr6-25050736-C-T

Variant summary

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

The ENST00000761912.1(ENSG00000288887):​n.734+25964C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 151,954 control chromosomes in the GnomAD database, including 26,764 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 (26764 hom., cov: 31)
• Consequence: ENSG00000288887 ENST00000761912.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822
• Publications: 0 publications found

Genes affected

ENSG00000229313 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000761912.1. 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
	ENSG00000229313	ENST00000428903.1	TSL:5	n.79-4227C>G		intron	N/A
	ENSG00000288887	ENST00000761912.1		n.734+25964C>G		intron	N/A
	ENSG00000285801	ENST00000762009.1		n.827+25722C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87234 AN: 151836 Hom.: 26754 Cov.: 31

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.574 AC: 87270 AN: 151954 Hom.: 26764 Cov.: 31 AF XY: 0.577 AC XY: 42863 AN XY: 74264

African (AFR) AF: 0.343 AC: 14200 AN: 41408

American (AMR) AF: 0.588 AC: 8984 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1958 AN: 3472

East Asian (EAS) AF: 0.737 AC: 3808 AN: 5168

South Asian (SAS) AF: 0.662 AC: 3186 AN: 4816

European-Finnish (FIN) AF: 0.701 AC: 7400 AN: 10552

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45726 AN: 67954

Other (OTH) AF: 0.571 AC: 1205 AN: 2112

Alfa AF: 0.501 Hom.: 1573

Bravo AF: 0.553

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.56
DANN	Benign	0.30
PhyloP100		-0.82

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: rs304256;

hg19: chr6-25050964;