10-78755324-A-G

Variant names:

• chr10-78755324-A-G
• rs7900239

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 0.837 in 152,050 control chromosomes in the GnomAD database, including 53,446 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 0.84 (53446 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.871 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: 0.837 AC: 127237 AN: 151932 Hom.: 53409 Cov.: 31

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.837 AC: 127322 AN: 152050 Hom.: 53446 Cov.: 31 AF XY: 0.830 AC XY: 61678 AN XY: 74300

African (AFR) AF: 0.809 AC: 33536 AN: 41470

American (AMR) AF: 0.797 AC: 12188 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 3126 AN: 3472

East Asian (EAS) AF: 0.733 AC: 3764 AN: 5138

South Asian (SAS) AF: 0.799 AC: 3843 AN: 4812

European-Finnish (FIN) AF: 0.799 AC: 8430 AN: 10554

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.877 AC: 59600 AN: 67996

Other (OTH) AF: 0.814 AC: 1717 AN: 2110

Alfa AF: 0.868 Hom.: 31260

Bravo AF: 0.838

Asia WGS AF: 0.725 AC: 2524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	21
DANN	Benign	0.55
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs7900239; hg19: chr10-80515081;