rs11000108

Variant names:

• chr10-71948342-T-C
• rs11000108

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 0.111 in 152,152 control chromosomes in the GnomAD database, including 1,080 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 0.11 (1080 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.137 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: 0.111 AC: 16862 AN: 152034 Hom.: 1081 Cov.: 31

Gnomad AFR AF: 0.0611

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.0884

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.111 AC: 16855 AN: 152152 Hom.: 1080 Cov.: 31 AF XY: 0.110 AC XY: 8170 AN XY: 74374

African (AFR) AF: 0.0610 AC: 2534 AN: 41520

American (AMR) AF: 0.0882 AC: 1349 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3466

East Asian (EAS) AF: 0.138 AC: 709 AN: 5154

South Asian (SAS) AF: 0.118 AC: 567 AN: 4814

European-Finnish (FIN) AF: 0.130 AC: 1379 AN: 10600

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9479 AN: 67992

Other (OTH) AF: 0.116 AC: 244 AN: 2108

Alfa AF: 0.128 Hom.: 2393

Bravo AF: 0.109

Asia WGS AF: 0.112 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.0
DANN	Benign	0.53
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs11000108; hg19: chr10-73708100;