rs1555082

Variant names:

• chr6-21346942-C-T
• rs1555082

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 0.464 in 151,950 control chromosomes in the GnomAD database, including 19,438 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 0.46 (19438 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263
• Publications: 2 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 (NFE) allele frequency at 95% confidence interval = 0.599 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: 0.465 AC: 70561 AN: 151832 Hom.: 19441 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.464 AC: 70565 AN: 151950 Hom.: 19438 Cov.: 32 AF XY: 0.467 AC XY: 34671 AN XY: 74248

African (AFR) AF: 0.154 AC: 6372 AN: 41454

American (AMR) AF: 0.601 AC: 9166 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1983 AN: 3470

East Asian (EAS) AF: 0.333 AC: 1716 AN: 5158

South Asian (SAS) AF: 0.487 AC: 2346 AN: 4820

European-Finnish (FIN) AF: 0.591 AC: 6218 AN: 10520

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41014 AN: 67958

Other (OTH) AF: 0.499 AC: 1051 AN: 2106

Alfa AF: 0.546 Hom.: 3384

Bravo AF: 0.447

Asia WGS AF: 0.391 AC: 1361 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	4.7
DANN	Benign	0.56
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs1555082; hg19: chr6-21347173;