6-52998902-T-C

Variant names:

• chr6-52998902-T-C
• rs7773621

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 0.303 in 151,860 control chromosomes in the GnomAD database, including 7,570 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 0.30 (7570 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 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: 0.303 AC: 45971 AN: 151740 Hom.: 7534 Cov.: 31

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.303 AC: 46040 AN: 151860 Hom.: 7570 Cov.: 31 AF XY: 0.297 AC XY: 22082 AN XY: 74228

African (AFR) AF: 0.421 AC: 17394 AN: 41348

American (AMR) AF: 0.253 AC: 3858 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1123 AN: 3460

East Asian (EAS) AF: 0.128 AC: 661 AN: 5168

South Asian (SAS) AF: 0.167 AC: 803 AN: 4816

European-Finnish (FIN) AF: 0.273 AC: 2876 AN: 10552

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18481 AN: 67954

Other (OTH) AF: 0.302 AC: 636 AN: 2106

Alfa AF: 0.302 Hom.: 2121

Bravo AF: 0.309

Asia WGS AF: 0.157 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.99
DANN	Benign	0.63
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs7773621; hg19: chr6-52863700;