chr10-100367735-A-G

Variant names:

• chr10-100367735-A-G
• rs575338

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 0.892 in 152,234 control chromosomes in the GnomAD database, including 60,819 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 0.89 (60819 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.892 AC: 135710 AN: 152116 Hom.: 60760 Cov.: 33

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.892 AC: 135829 AN: 152234 Hom.: 60819 Cov.: 33 AF XY: 0.895 AC XY: 66633 AN XY: 74426

African (AFR) AF: 0.942 AC: 39159 AN: 41560

American (AMR) AF: 0.882 AC: 13495 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.837 AC: 2904 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5189 AN: 5194

South Asian (SAS) AF: 0.968 AC: 4674 AN: 4828

European-Finnish (FIN) AF: 0.869 AC: 9167 AN: 10548

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.857 AC: 58296 AN: 68022

Other (OTH) AF: 0.879 AC: 1858 AN: 2114

Alfa AF: 0.868 Hom.: 18756

Bravo AF: 0.893

Asia WGS AF: 0.973 AC: 3378 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.80
DANN	Benign	0.36
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs575338; hg19: chr10-102127492;