rs7083920

Variant names:

• chr10-44576442-C-T
• rs7083920

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 0.437 in 152,114 control chromosomes in the GnomAD database, including 15,041 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 0.44 (15041 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 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: 0.437 AC: 66421 AN: 151996 Hom.: 15023 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.437 AC: 66488 AN: 152114 Hom.: 15041 Cov.: 32 AF XY: 0.440 AC XY: 32710 AN XY: 74354

African (AFR) AF: 0.324 AC: 13447 AN: 41512

American (AMR) AF: 0.497 AC: 7597 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1351 AN: 3470

East Asian (EAS) AF: 0.448 AC: 2313 AN: 5166

South Asian (SAS) AF: 0.511 AC: 2465 AN: 4822

European-Finnish (FIN) AF: 0.502 AC: 5301 AN: 10566

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.478 AC: 32464 AN: 67978

Other (OTH) AF: 0.444 AC: 937 AN: 2112

Alfa AF: 0.453 Hom.: 2621

Bravo AF: 0.435

Asia WGS AF: 0.497 AC: 1730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.59
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs7083920; hg19: chr10-45071890;