rs16975985

Variant names:

• chr17-70637924-A-G
• rs16975985

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.12 in 152,140 control chromosomes in the GnomAD database, including 1,490 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 0.12 (1490 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.939

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 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: 0.120 AC: 18255 AN: 152022 Hom.: 1489 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.0877

Gnomad ASJ AF: 0.0568

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0710

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0676

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.120 AC: 18259 AN: 152140 Hom.: 1490 Cov.: 32 AF XY: 0.120 AC XY: 8927 AN XY: 74378

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.0875

Gnomad4 ASJ AF: 0.0568

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.0706

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.0675

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0804 Hom.: 604

Bravo AF: 0.123

Asia WGS AF: 0.0920 AC: 321 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.8
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16975985; hg19: chr17-68634065;