rs788076

Variant names:

• chr10-29047920-G-A
• rs788076

Your query was ambiguous. Multiple possible variants found:

• chr10-29047920-G-A
• chr10-29047920-G-T

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 0.928 in 152,256 control chromosomes in the GnomAD database, including 66,025 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 0.93 (66025 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.928 AC: 141252 AN: 152140 Hom.: 65986 Cov.: 32

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.996

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.979

Gnomad OTH AF: 0.915

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

GnomAD4 genome AF: 0.928 AC: 141349 AN: 152256 Hom.: 66025 Cov.: 32 AF XY: 0.930 AC XY: 69255 AN XY: 74448

African (AFR) AF: 0.811 AC: 33681 AN: 41508

American (AMR) AF: 0.943 AC: 14427 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3126 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5183 AN: 5184

South Asian (SAS) AF: 0.996 AC: 4804 AN: 4824

European-Finnish (FIN) AF: 0.983 AC: 10435 AN: 10616

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.979 AC: 66614 AN: 68034

Other (OTH) AF: 0.916 AC: 1937 AN: 2114

Alfa AF: 0.956 Hom.: 202869

Bravo AF: 0.920

Asia WGS AF: 0.982 AC: 3416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.53
DANN	Benign	0.48
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs788076; hg19: chr10-29336849;