10-77647022-T-C

Variant names:

• chr10-77647022-T-C
• rs2244688

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 0.781 in 152,224 control chromosomes in the GnomAD database, including 46,974 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 0.78 (46974 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118801 AN: 152106 Hom.: 46925 Cov.: 33

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.781 AC: 118904 AN: 152224 Hom.: 46974 Cov.: 33 AF XY: 0.784 AC XY: 58311 AN XY: 74414

African (AFR) AF: 0.901 AC: 37454 AN: 41548

American (AMR) AF: 0.766 AC: 11716 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2451 AN: 3470

East Asian (EAS) AF: 0.762 AC: 3938 AN: 5166

South Asian (SAS) AF: 0.730 AC: 3520 AN: 4820

European-Finnish (FIN) AF: 0.801 AC: 8491 AN: 10600

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48804 AN: 68000

Other (OTH) AF: 0.780 AC: 1651 AN: 2116

Alfa AF: 0.737 Hom.: 55461

Bravo AF: 0.783

Asia WGS AF: 0.756 AC: 2630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.023
DANN	Benign	0.39
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs2244688; hg19: chr10-79406780;