17-61418877-T-C

Variant names:

• chr17-61418877-T-C
• rs9905140

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 0.469 in 152,118 control chromosomes in the GnomAD database, including 19,159 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 0.47 (19159 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.603 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: 0.469 AC: 71300 AN: 151998 Hom.: 19156 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.469 AC: 71312 AN: 152118 Hom.: 19159 Cov.: 32 AF XY: 0.471 AC XY: 34987 AN XY: 74356

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.494

Alfa AF: 0.582 Hom.: 33651

Bravo AF: 0.442

Asia WGS AF: 0.409 AC: 1427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9905140; hg19: chr17-59496238;