6-66219155-C-T

Variant names:

• chr6-66219155-C-T
• rs3857536

Variant summary

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

The variant allele was found at a frequency of 0.589 in 151,870 control chromosomes in the GnomAD database, including 26,862 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 0.59 (26862 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 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

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89412 AN: 151752 Hom.: 26825 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.589 AC: 89505 AN: 151870 Hom.: 26862 Cov.: 32 AF XY: 0.588 AC XY: 43594 AN XY: 74200

African (AFR) AF: 0.690 AC: 28597 AN: 41450

American (AMR) AF: 0.548 AC: 8368 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1761 AN: 3468

East Asian (EAS) AF: 0.642 AC: 3305 AN: 5150

South Asian (SAS) AF: 0.587 AC: 2836 AN: 4830

European-Finnish (FIN) AF: 0.494 AC: 5198 AN: 10532

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37465 AN: 67874

Other (OTH) AF: 0.576 AC: 1210 AN: 2102

Alfa AF: 0.579 Hom.: 7433

Bravo AF: 0.598

Asia WGS AF: 0.585 AC: 2029 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.5
DANN	Benign	0.39
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs3857536; hg19: chr6-66929048;