6-31451610-T-C

Variant names:

• chr6-31451610-T-C
• rs2516458
• ENST00000673857.1:n.63-11513T>C

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.63-11513T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,700 control chromosomes in the GnomAD database, including 20,588 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 0.51 (20588 hom., cov: 32)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 7 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.56 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.63-11513T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77483 AN: 151582 Hom.: 20554 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.511 AC: 77556 AN: 151700 Hom.: 20588 Cov.: 32 AF XY: 0.506 AC XY: 37535 AN XY: 74170

African (AFR) AF: 0.566 AC: 23361 AN: 41280

American (AMR) AF: 0.545 AC: 8283 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1945 AN: 3466

East Asian (EAS) AF: 0.210 AC: 1086 AN: 5170

South Asian (SAS) AF: 0.439 AC: 2112 AN: 4810

European-Finnish (FIN) AF: 0.494 AC: 5216 AN: 10554

Middle Eastern (MID) AF: 0.462 AC: 134 AN: 290

European-Non Finnish (NFE) AF: 0.497 AC: 33751 AN: 67924

Other (OTH) AF: 0.516 AC: 1086 AN: 2106

Alfa AF: 0.502 Hom.: 14530

Bravo AF: 0.518

Asia WGS AF: 0.340 AC: 1180 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.53
PhyloP100		-1.4

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: rs2516458;

hg19: chr6-31419387;