17-49962977-T-C

Variant names:

• chr17-49962977-T-C
• rs985626

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 0.87 in 152,148 control chromosomes in the GnomAD database, including 58,354 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 0.87 (58354 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.870 AC: 132312 AN: 152030 Hom.: 58325 Cov.: 31

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.923

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.972

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.870 AC: 132397 AN: 152148 Hom.: 58354 Cov.: 31 AF XY: 0.870 AC XY: 64729 AN XY: 74386

African (AFR) AF: 0.718 AC: 29770 AN: 41472

American (AMR) AF: 0.923 AC: 14119 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3128 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5157 AN: 5164

South Asian (SAS) AF: 0.972 AC: 4689 AN: 4822

European-Finnish (FIN) AF: 0.901 AC: 9541 AN: 10594

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.927 AC: 63063 AN: 68006

Other (OTH) AF: 0.868 AC: 1833 AN: 2112

Alfa AF: 0.906 Hom.: 43844

Bravo AF: 0.864

Asia WGS AF: 0.952 AC: 3309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.81
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs985626; hg19: chr17-48040341;