rs180075

Variant names:

• chr17-69958971-T-C
• rs180075

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 0.733 in 152,116 control chromosomes in the GnomAD database, including 41,154 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 0.73 (41154 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 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: 0.732 AC: 111317 AN: 151998 Hom.: 41104 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.733 AC: 111427 AN: 152116 Hom.: 41154 Cov.: 32 AF XY: 0.736 AC XY: 54742 AN XY: 74358

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.734

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.850

Gnomad4 FIN AF: 0.698

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.716

Alfa AF: 0.698 Hom.: 4621

Bravo AF: 0.739

Asia WGS AF: 0.895 AC: 3112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.82
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs180075; hg19: chr17-67955112;