chr6-33156916-G-C

Variant names:

• chr6-33156916-G-C
• rs3130159

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 0.155 in 152,108 control chromosomes in the GnomAD database, including 2,089 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 0.16 (2089 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 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: 0.155 AC: 23549 AN: 151990 Hom.: 2079 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.155 AC: 23590 AN: 152108 Hom.: 2089 Cov.: 31 AF XY: 0.155 AC XY: 11528 AN XY: 74356

African (AFR) AF: 0.236 AC: 9764 AN: 41456

American (AMR) AF: 0.103 AC: 1579 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0807 AC: 280 AN: 3470

East Asian (EAS) AF: 0.127 AC: 659 AN: 5188

South Asian (SAS) AF: 0.159 AC: 769 AN: 4824

European-Finnish (FIN) AF: 0.151 AC: 1599 AN: 10586

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8593 AN: 67998

Other (OTH) AF: 0.134 AC: 283 AN: 2110

Alfa AF: 0.138 Hom.: 182

Bravo AF: 0.154

Asia WGS AF: 0.171 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.53
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs3130159; hg19: chr6-33124693;