chr6-90511765-C-G

Variant names:

• chr6-90511765-C-G
• rs157693

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 0.448 in 151,832 control chromosomes in the GnomAD database, including 15,667 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 0.45 (15667 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 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: 0.448 AC: 67979 AN: 151714 Hom.: 15654 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.448 AC: 68049 AN: 151832 Hom.: 15667 Cov.: 32 AF XY: 0.443 AC XY: 32875 AN XY: 74206

African (AFR) AF: 0.552 AC: 22829 AN: 41382

American (AMR) AF: 0.444 AC: 6782 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1922 AN: 3470

East Asian (EAS) AF: 0.369 AC: 1904 AN: 5158

South Asian (SAS) AF: 0.543 AC: 2617 AN: 4816

European-Finnish (FIN) AF: 0.310 AC: 3263 AN: 10528

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27220 AN: 67906

Other (OTH) AF: 0.493 AC: 1038 AN: 2106

Alfa AF: 0.274 Hom.: 593

Bravo AF: 0.459

Asia WGS AF: 0.471 AC: 1643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.96
DANN	Benign	0.45
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs157693; hg19: chr6-91221484; COSMIC: COSV65223894;