chr10-58319035-G-A

Variant names:

• chr10-58319035-G-A
• rs7072568

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 0.0895 in 152,144 control chromosomes in the GnomAD database, including 643 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 0.090 (643 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 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: 0.0894 AC: 13598 AN: 152026 Hom.: 640 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.0798

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.0932

Gnomad SAS AF: 0.0406

Gnomad FIN AF: 0.0642

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0726

Gnomad OTH AF: 0.0832

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

GnomAD4 genome AF: 0.0895 AC: 13621 AN: 152144 Hom.: 643 Cov.: 32 AF XY: 0.0871 AC XY: 6478 AN XY: 74384

African (AFR) AF: 0.132 AC: 5469 AN: 41480

American (AMR) AF: 0.0800 AC: 1223 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 369 AN: 3472

East Asian (EAS) AF: 0.0933 AC: 482 AN: 5168

South Asian (SAS) AF: 0.0409 AC: 197 AN: 4820

European-Finnish (FIN) AF: 0.0642 AC: 680 AN: 10586

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0725 AC: 4934 AN: 68018

Other (OTH) AF: 0.0903 AC: 191 AN: 2114

Alfa AF: 0.0824 Hom.: 972

Bravo AF: 0.0939

Asia WGS AF: 0.0890 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	5.0
DANN	Benign	0.58
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs7072568; hg19: chr10-60078795;