rs6585740

Positions:

• chr10-121468695-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.245

Alfa AF: 0.239 Hom.: 2564

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6585740; hg19: chr10-123228209;