chr6-151650552-G-A

Variant names:

• chr6-151650552-G-A
• rs851974

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 0.625 in 152,026 control chromosomes in the GnomAD database, including 31,101 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 0.62 (31101 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 9 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 = 0.823 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: 0.624 AC: 94848 AN: 151908 Hom.: 31053 Cov.: 31

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.625 AC: 94952 AN: 152026 Hom.: 31101 Cov.: 31 AF XY: 0.616 AC XY: 45758 AN XY: 74300

African (AFR) AF: 0.830 AC: 34456 AN: 41504

American (AMR) AF: 0.472 AC: 7220 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2194 AN: 3470

East Asian (EAS) AF: 0.416 AC: 2139 AN: 5148

South Asian (SAS) AF: 0.577 AC: 2782 AN: 4824

European-Finnish (FIN) AF: 0.499 AC: 5247 AN: 10524

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 38998 AN: 67956

Other (OTH) AF: 0.612 AC: 1292 AN: 2110

Alfa AF: 0.572 Hom.: 14426

Bravo AF: 0.630

Asia WGS AF: 0.553 AC: 1924 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	0.43
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs851974; hg19: chr6-151971687; COSMIC: COSV107167828;