rs836554

Variant names:

• chr7-6405604-C-T
• rs836554

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 0.428 in 150,228 control chromosomes in the GnomAD database, including 18,089 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 0.43 (18089 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.754 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: 0.428 AC: 64228 AN: 150118 Hom.: 18031 Cov.: 29

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.428 AC: 64346 AN: 150228 Hom.: 18089 Cov.: 29 AF XY: 0.435 AC XY: 31868 AN XY: 73234

African (AFR) AF: 0.761 AC: 31030 AN: 40774

American (AMR) AF: 0.476 AC: 7155 AN: 15044

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 800 AN: 3456

East Asian (EAS) AF: 0.748 AC: 3782 AN: 5058

South Asian (SAS) AF: 0.490 AC: 2339 AN: 4770

European-Finnish (FIN) AF: 0.259 AC: 2610 AN: 10078

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.226 AC: 15306 AN: 67762

Other (OTH) AF: 0.410 AC: 856 AN: 2088

Alfa AF: 0.387 Hom.: 6317

Bravo AF: 0.459

Asia WGS AF: 0.651 AC: 2262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.40
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs836554; hg19: chr7-6445235;