17-49201163-G-A

Variant names:

• chr17-49201163-G-A
• rs8077444

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 0.217 in 152,142 control chromosomes in the GnomAD database, including 4,016 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 0.22 (4016 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33019 AN: 152024 Hom.: 4003 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.217 AC: 33066 AN: 152142 Hom.: 4016 Cov.: 32 AF XY: 0.219 AC XY: 16284 AN XY: 74368

African (AFR) AF: 0.246 AC: 10228 AN: 41494

American (AMR) AF: 0.281 AC: 4300 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 760 AN: 3472

East Asian (EAS) AF: 0.454 AC: 2342 AN: 5154

South Asian (SAS) AF: 0.203 AC: 979 AN: 4822

European-Finnish (FIN) AF: 0.112 AC: 1184 AN: 10610

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12552 AN: 67990

Other (OTH) AF: 0.222 AC: 468 AN: 2112

Alfa AF: 0.190 Hom.: 3350

Bravo AF: 0.234

Asia WGS AF: 0.304 AC: 1056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
DANN	Benign	0.72
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs8077444; hg19: chr17-47278525;