10-59779644-G-T

Variant names:

• chr10-59779644-G-T
• rs721992

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 0.499 in 151,832 control chromosomes in the GnomAD database, including 20,113 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 0.50 (20113 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 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: 0.499 AC: 75719 AN: 151714 Hom.: 20075 Cov.: 30

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.499 AC: 75795 AN: 151832 Hom.: 20113 Cov.: 30 AF XY: 0.497 AC XY: 36878 AN XY: 74178

African (AFR) AF: 0.691 AC: 28595 AN: 41410

American (AMR) AF: 0.415 AC: 6335 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1612 AN: 3462

East Asian (EAS) AF: 0.300 AC: 1549 AN: 5158

South Asian (SAS) AF: 0.475 AC: 2274 AN: 4784

European-Finnish (FIN) AF: 0.454 AC: 4784 AN: 10536

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29037 AN: 67920

Other (OTH) AF: 0.475 AC: 1000 AN: 2106

Alfa AF: 0.421 Hom.: 8455

Bravo AF: 0.501

Asia WGS AF: 0.415 AC: 1443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.19
DANN	Benign	0.49
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs721992; hg19: chr10-61539402;