chr10-77767860-G-A

Variant names:

• chr10-77767860-G-A
• rs1344967

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 0.257 in 152,106 control chromosomes in the GnomAD database, including 5,602 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 0.26 (5602 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39073 AN: 151988 Hom.: 5590 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.257 AC: 39116 AN: 152106 Hom.: 5602 Cov.: 32 AF XY: 0.262 AC XY: 19468 AN XY: 74330

African (AFR) AF: 0.150 AC: 6238 AN: 41516

American (AMR) AF: 0.393 AC: 5999 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 650 AN: 3470

East Asian (EAS) AF: 0.302 AC: 1566 AN: 5178

South Asian (SAS) AF: 0.305 AC: 1470 AN: 4818

European-Finnish (FIN) AF: 0.309 AC: 3262 AN: 10540

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19150 AN: 67984

Other (OTH) AF: 0.251 AC: 530 AN: 2112

Alfa AF: 0.156 Hom.: 355

Bravo AF: 0.257

Asia WGS AF: 0.316 AC: 1101 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1344967; hg19: chr10-79527618;