6-31420094-G-C

Variant names:

• chr6-31420094-G-C
• rs2596532
• ENST00000673857.1:n.62+19331G>C

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.62+19331G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 151,796 control chromosomes in the GnomAD database, including 1,331 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 0.11 (1331 hom., cov: 31)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 21 publications found

Genes affected

ENSG00000288587 (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 (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000673857.1. 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
	ENSG00000288587	ENST00000673857.1		n.62+19331G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16243 AN: 151678 Hom.: 1325 Cov.: 31

Gnomad AFR AF: 0.0284

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.107 AC: 16251 AN: 151796 Hom.: 1331 Cov.: 31 AF XY: 0.114 AC XY: 8476 AN XY: 74220

African (AFR) AF: 0.0283 AC: 1170 AN: 41312

American (AMR) AF: 0.171 AC: 2601 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 504 AN: 3472

East Asian (EAS) AF: 0.345 AC: 1771 AN: 5130

South Asian (SAS) AF: 0.212 AC: 1016 AN: 4790

European-Finnish (FIN) AF: 0.151 AC: 1597 AN: 10586

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7278 AN: 67992

Other (OTH) AF: 0.115 AC: 243 AN: 2112

Alfa AF: 0.0552 Hom.: 67

Bravo AF: 0.106

Asia WGS AF: 0.269 AC: 936 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	4.3
DANN	Benign	0.30
PhyloP100		0.21

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: rs2596532;

hg19: chr6-31387871;