10-77647022-T-C

Variant names:

• chr10-77647022-T-C
• rs2244688

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 0.781 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.781 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

Gnomad4 AFR AF: 0.901

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.801

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.780

Alfa AF: 0.730 Hom.: 42095

Bravo AF: 0.783

Asia WGS AF: 0.756 AC: 2630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2244688; hg19: chr10-79406780;