rs6537571

Variant names:

• chr10-48678768-C-T
• rs6537571

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 0.39 in 152,054 control chromosomes in the GnomAD database, including 12,304 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 0.39 (12304 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.664
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.528 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: 0.390 AC: 59203 AN: 151936 Hom.: 12273 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.390 AC: 59283 AN: 152054 Hom.: 12304 Cov.: 32 AF XY: 0.385 AC XY: 28650 AN XY: 74322

African (AFR) AF: 0.534 AC: 22132 AN: 41466

American (AMR) AF: 0.368 AC: 5626 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1317 AN: 3472

East Asian (EAS) AF: 0.261 AC: 1352 AN: 5178

South Asian (SAS) AF: 0.307 AC: 1473 AN: 4804

European-Finnish (FIN) AF: 0.262 AC: 2767 AN: 10580

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23419 AN: 67962

Other (OTH) AF: 0.414 AC: 876 AN: 2116

Alfa AF: 0.368 Hom.: 26705

Bravo AF: 0.400

Asia WGS AF: 0.356 AC: 1235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.1
DANN	Benign	0.26
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs6537571; hg19: chr10-49886813;