rs10911902

Variant names:

• chr1-186663185-C-T
• rs10911902

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 0.137 in 152,078 control chromosomes in the GnomAD database, including 1,825 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 0.14 (1825 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.188 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: 0.137 AC: 20814 AN: 151960 Hom.: 1826 Cov.: 32

Gnomad AFR AF: 0.0337

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.137 AC: 20810 AN: 152078 Hom.: 1825 Cov.: 32 AF XY: 0.138 AC XY: 10260 AN XY: 74320

African (AFR) AF: 0.0336 AC: 1397 AN: 41518

American (AMR) AF: 0.121 AC: 1844 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 358 AN: 3468

East Asian (EAS) AF: 0.144 AC: 743 AN: 5176

South Asian (SAS) AF: 0.198 AC: 956 AN: 4818

European-Finnish (FIN) AF: 0.213 AC: 2251 AN: 10546

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12875 AN: 67958

Other (OTH) AF: 0.106 AC: 223 AN: 2112

Alfa AF: 0.166 Hom.: 5286

Bravo AF: 0.123

Asia WGS AF: 0.148 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.7
DANN	Benign	0.28
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs10911902; hg19: chr1-186632317;