rs555985

Variant names:

• chr6-152897587-C-A
• rs555985

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.539 in 151,934 control chromosomes in the GnomAD database, including 22,623 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 0.54 (22623 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.594

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.64 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: 0.539 AC: 81821 AN: 151814 Hom.: 22587 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.539 AC: 81912 AN: 151934 Hom.: 22623 Cov.: 32 AF XY: 0.542 AC XY: 40218 AN XY: 74222

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.517

Alfa AF: 0.512 Hom.: 3417

Bravo AF: 0.552

Asia WGS AF: 0.605 AC: 2100 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs555985; hg19: chr6-153218722; COSMIC: COSV69403971;