rs642858

Variant names:

• chr6-139952510-G-A
• rs642858
• ENST00000666152.1:n.748-13052C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-139952510-G-A
• chr6-139952510-G-C
• chr6-139952510-G-T

Variant summary

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

The ENST00000666152.1(ENSG00000287820):​n.748-13052C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 151,904 control chromosomes in the GnomAD database, including 4,216 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 0.22 (4216 hom., cov: 32)
• Consequence: ENSG00000287820 ENST00000666152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335

Genes affected

ENSG00000287820 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 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
ENSG00000287820	ENST00000666152.1	n.748-13052C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33895 AN: 151786 Hom.: 4209 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.223 AC: 33933 AN: 151904 Hom.: 4216 Cov.: 32 AF XY: 0.225 AC XY: 16743 AN XY: 74256

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.267

Alfa AF: 0.252 Hom.: 7435

Bravo AF: 0.225

Asia WGS AF: 0.395 AC: 1362 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs642858; hg19: chr6-140273647; COSMIC: COSV60287441;