chr17-75861301-C-G

Variant names:

• chr17-75861301-C-G
• rs11869977

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 0.276 in 152,162 control chromosomes in the GnomAD database, including 7,560 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 0.28 (7560 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.507 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: 0.276 AC: 41894 AN: 152044 Hom.: 7523 Cov.: 33

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.276 AC: 41989 AN: 152162 Hom.: 7560 Cov.: 33 AF XY: 0.270 AC XY: 20089 AN XY: 74392

African (AFR) AF: 0.513 AC: 21254 AN: 41464

American (AMR) AF: 0.209 AC: 3192 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 733 AN: 3470

East Asian (EAS) AF: 0.138 AC: 713 AN: 5172

South Asian (SAS) AF: 0.197 AC: 954 AN: 4832

European-Finnish (FIN) AF: 0.115 AC: 1225 AN: 10612

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13135 AN: 68018

Other (OTH) AF: 0.284 AC: 600 AN: 2112

Alfa AF: 0.101 Hom.: 148

Bravo AF: 0.293

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.65
DANN	Benign	0.65
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs11869977; hg19: chr17-73857382;