chr17-65524661-G-A

Variant names:

• chr17-65524661-G-A
• rs12452196

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 0.113 in 152,238 control chromosomes in the GnomAD database, including 1,171 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 (1171 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.359
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 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: 0.113 AC: 17179 AN: 152120 Hom.: 1173 Cov.: 31

Gnomad AFR AF: 0.0648

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.0389

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0988

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.113 AC: 17177 AN: 152238 Hom.: 1171 Cov.: 31 AF XY: 0.112 AC XY: 8335 AN XY: 74430

African (AFR) AF: 0.0647 AC: 2687 AN: 41552

American (AMR) AF: 0.105 AC: 1599 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 976 AN: 3470

East Asian (EAS) AF: 0.0392 AC: 203 AN: 5176

South Asian (SAS) AF: 0.130 AC: 626 AN: 4816

European-Finnish (FIN) AF: 0.0988 AC: 1048 AN: 10612

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.141 AC: 9594 AN: 68002

Other (OTH) AF: 0.138 AC: 291 AN: 2116

Alfa AF: 0.126 Hom.: 1737

Bravo AF: 0.112

Asia WGS AF: 0.0760 AC: 265 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	6.2
DANN	Benign	0.61
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs12452196; hg19: chr17-63520779;