17-49202400-G-T

Variant names:

• chr17-49202400-G-T
• rs11868965

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 152,106 control chromosomes in the GnomAD database, including 3,999 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 (3999 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

Selected	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: 32979 AN: 151988 Hom.: 3986 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.217 AC: 33026 AN: 152106 Hom.: 3999 Cov.: 32 AF XY: 0.218 AC XY: 16246 AN XY: 74372

African (AFR) AF: 0.247 AC: 10236 AN: 41482

American (AMR) AF: 0.282 AC: 4300 AN: 15272

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

East Asian (EAS) AF: 0.443 AC: 2285 AN: 5154

South Asian (SAS) AF: 0.203 AC: 977 AN: 4810

European-Finnish (FIN) AF: 0.112 AC: 1188 AN: 10610

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

European-Non Finnish (NFE) AF: 0.185 AC: 12561 AN: 67994

Other (OTH) AF: 0.221 AC: 467 AN: 2110

Alfa AF: 0.202 Hom.: 13282

Bravo AF: 0.233

Asia WGS AF: 0.301 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.73
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs11868965; hg19: chr17-47279762;