rs11651000

Variant names:

• chr17-47757912-G-A
• rs11651000

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 0.138 in 152,190 control chromosomes in the GnomAD database, including 1,586 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 (1586 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 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: 0.138 AC: 20984 AN: 152072 Hom.: 1589 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.0113

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.138 AC: 20988 AN: 152190 Hom.: 1586 Cov.: 32 AF XY: 0.136 AC XY: 10124 AN XY: 74402

African (AFR) AF: 0.119 AC: 4953 AN: 41512

American (AMR) AF: 0.124 AC: 1901 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3470

East Asian (EAS) AF: 0.0116 AC: 60 AN: 5190

South Asian (SAS) AF: 0.133 AC: 643 AN: 4824

European-Finnish (FIN) AF: 0.146 AC: 1542 AN: 10574

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10868 AN: 68010

Other (OTH) AF: 0.136 AC: 287 AN: 2110

Alfa AF: 0.148 Hom.: 2920

Bravo AF: 0.136

Asia WGS AF: 0.0690 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.41
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs11651000; hg19: chr17-45835278;