chr6-139952510-G-A

Variant names:

• chr6-139952510-G-A
• rs642858
• ENST00000666152.2:n.748-13052C>T

Variant summary

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

The ENST00000666152.2(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 ENST00000666152.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335
• Publications: 26 publications found

Genes affected

ENSG00000287820 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000666152.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287820	ENST00000666152.2		n.748-13052C>T		intron	N/A

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

African (AFR) AF: 0.160 AC: 6653 AN: 41458

American (AMR) AF: 0.212 AC: 3245 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1294 AN: 3472

East Asian (EAS) AF: 0.421 AC: 2172 AN: 5154

South Asian (SAS) AF: 0.373 AC: 1791 AN: 4808

European-Finnish (FIN) AF: 0.171 AC: 1803 AN: 10530

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16019 AN: 67896

Other (OTH) AF: 0.267 AC: 561 AN: 2102

Alfa AF: 0.242 Hom.: 15779

Bravo AF: 0.225

Asia WGS AF: 0.395 AC: 1362 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.5
DANN	Benign	0.57
PhyloP100		0.34

Splicing

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

Other links and lift over

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