rs7073842

Variant names:

• chr10-79896644-T-C
• rs7073842

Your query was ambiguous. Multiple possible variants found:

• chr10-79896644-T-C
• chr10-79896644-T-G

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 0.68 in 148,886 control chromosomes in the GnomAD database, including 35,447 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 0.68 (35447 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 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: 0.679 AC: 101077 AN: 148782 Hom.: 35384 Cov.: 25

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.680 AC: 101200 AN: 148886 Hom.: 35447 Cov.: 25 AF XY: 0.681 AC XY: 49241 AN XY: 72334

African (AFR) AF: 0.840 AC: 33848 AN: 40282

American (AMR) AF: 0.649 AC: 9619 AN: 14810

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2182 AN: 3468

East Asian (EAS) AF: 0.778 AC: 3919 AN: 5040

South Asian (SAS) AF: 0.743 AC: 3539 AN: 4764

European-Finnish (FIN) AF: 0.577 AC: 5527 AN: 9578

Middle Eastern (MID) AF: 0.682 AC: 195 AN: 286

European-Non Finnish (NFE) AF: 0.597 AC: 40422 AN: 67680

Other (OTH) AF: 0.673 AC: 1394 AN: 2072

Alfa AF: 0.613 Hom.: 45191

Bravo AF: 0.690

Asia WGS AF: 0.779 AC: 2708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.9
DANN	Benign	0.23
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7073842; hg19: chr10-81656400;