chr10-111083327-C-A

Variant names:

• chr10-111083327-C-A
• rs602618

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 0.582 in 152,086 control chromosomes in the GnomAD database, including 28,550 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 0.58 (28550 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.723 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: 0.583 AC: 88570 AN: 151968 Hom.: 28562 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.582 AC: 88577 AN: 152086 Hom.: 28550 Cov.: 32 AF XY: 0.580 AC XY: 43105 AN XY: 74344

African (AFR) AF: 0.321 AC: 13303 AN: 41466

American (AMR) AF: 0.613 AC: 9372 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2493 AN: 3464

East Asian (EAS) AF: 0.330 AC: 1709 AN: 5178

South Asian (SAS) AF: 0.458 AC: 2205 AN: 4816

European-Finnish (FIN) AF: 0.741 AC: 7835 AN: 10578

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.729 AC: 49537 AN: 67984

Other (OTH) AF: 0.591 AC: 1250 AN: 2114

Alfa AF: 0.693 Hom.: 59280

Bravo AF: 0.565

Asia WGS AF: 0.367 AC: 1277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.42
DANN	Benign	0.48
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs602618; hg19: chr10-112843085;