10-111764613-T-C

Variant names:

• chr10-111764613-T-C
• rs6585111

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 0.842 in 152,106 control chromosomes in the GnomAD database, including 54,880 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 0.84 (54880 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.927 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: 0.842 AC: 128017 AN: 151988 Hom.: 54859 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.878

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.935

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.842 AC: 128084 AN: 152106 Hom.: 54880 Cov.: 32 AF XY: 0.842 AC XY: 62577 AN XY: 74346

African (AFR) AF: 0.674 AC: 27946 AN: 41474

American (AMR) AF: 0.852 AC: 13021 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.878 AC: 3049 AN: 3472

East Asian (EAS) AF: 0.801 AC: 4128 AN: 5152

South Asian (SAS) AF: 0.765 AC: 3689 AN: 4822

European-Finnish (FIN) AF: 0.935 AC: 9919 AN: 10612

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.933 AC: 63422 AN: 67988

Other (OTH) AF: 0.848 AC: 1785 AN: 2106

Alfa AF: 0.900 Hom.: 229014

Bravo AF: 0.831

Asia WGS AF: 0.763 AC: 2656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	15
DANN	Benign	0.61
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs6585111; hg19: chr10-113524371;