rs6585740

Variant names:

• chr10-121468695-T-G
• rs6585740

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 0.243 in 152,150 control chromosomes in the GnomAD database, including 4,557 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 0.24 (4557 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.31
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.348 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: 0.243 AC: 36945 AN: 152032 Hom.: 4558 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.243 AC: 36960 AN: 152150 Hom.: 4557 Cov.: 32 AF XY: 0.242 AC XY: 17974 AN XY: 74382

African (AFR) AF: 0.259 AC: 10740 AN: 41526

American (AMR) AF: 0.240 AC: 3668 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 933 AN: 3468

East Asian (EAS) AF: 0.362 AC: 1868 AN: 5158

South Asian (SAS) AF: 0.317 AC: 1527 AN: 4818

European-Finnish (FIN) AF: 0.162 AC: 1718 AN: 10590

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15642 AN: 67980

Other (OTH) AF: 0.245 AC: 518 AN: 2112

Alfa AF: 0.239 Hom.: 3638

Bravo AF: 0.249

Asia WGS AF: 0.301 AC: 1046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.79
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs6585740; hg19: chr10-123228209;