chr6-132550514-A-C

Variant names:

• chr6-132550514-A-C
• rs1933988

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 0.389 in 152,112 control chromosomes in the GnomAD database, including 11,878 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 0.39 (11878 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 5 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 = 0.42 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: 0.389 AC: 59140 AN: 151992 Hom.: 11864 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.389 AC: 59204 AN: 152112 Hom.: 11878 Cov.: 32 AF XY: 0.388 AC XY: 28833 AN XY: 74360

African (AFR) AF: 0.425 AC: 17649 AN: 41484

American (AMR) AF: 0.378 AC: 5785 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1069 AN: 3470

East Asian (EAS) AF: 0.145 AC: 751 AN: 5180

South Asian (SAS) AF: 0.281 AC: 1354 AN: 4820

European-Finnish (FIN) AF: 0.499 AC: 5261 AN: 10546

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26127 AN: 67994

Other (OTH) AF: 0.364 AC: 769 AN: 2114

Alfa AF: 0.376 Hom.: 18362

Bravo AF: 0.379

Asia WGS AF: 0.220 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.43
DANN	Benign	0.51
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1933988; hg19: chr6-132871653;