rs2523685

Variant names:

• chr6-31458479-G-C
• rs2523685
• ENST00000673857.1:n.63-4644G>C

Your query was ambiguous. Multiple possible variants found:

• chr6-31458479-G-C
• chr6-31458479-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000673857.1(ENSG00000288587):​n.63-4644G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 151,502 control chromosomes in the GnomAD database, including 9,257 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 0.32 (9257 hom., cov: 32)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

Genes affected

ENSG00000288587 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.483 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
ENSG00000288587	ENST00000673857.1	n.63-4644G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48741 AN: 151386 Hom.: 9220 Cov.: 32

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.322 AC: 48825 AN: 151502 Hom.: 9257 Cov.: 32 AF XY: 0.325 AC XY: 24048 AN XY: 74048

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.361

Alfa AF: 0.142 Hom.: 272

Bravo AF: 0.341

Asia WGS AF: 0.303 AC: 1046 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.17
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2523685; hg19: chr6-31426256;