17-65527485-G-C

Variant names:

• chr17-65527485-G-C
• rs11868547

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 0.374 in 152,040 control chromosomes in the GnomAD database, including 11,951 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 0.37 (11951 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.457 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: 0.374 AC: 56829 AN: 151922 Hom.: 11952 Cov.: 31

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.374 AC: 56834 AN: 152040 Hom.: 11951 Cov.: 31 AF XY: 0.374 AC XY: 27808 AN XY: 74300

African (AFR) AF: 0.176 AC: 7314 AN: 41512

American (AMR) AF: 0.421 AC: 6419 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1334 AN: 3468

East Asian (EAS) AF: 0.325 AC: 1675 AN: 5150

South Asian (SAS) AF: 0.434 AC: 2089 AN: 4810

European-Finnish (FIN) AF: 0.494 AC: 5211 AN: 10554

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.462 AC: 31375 AN: 67974

Other (OTH) AF: 0.362 AC: 763 AN: 2110

Alfa AF: 0.302 Hom.: 903

Bravo AF: 0.362

Asia WGS AF: 0.347 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.30
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs11868547; hg19: chr17-63523603;