chr5-175445201-G-T

Variant names:

• chr5-175445201-G-T
• rs10063995

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 0.0665 in 152,210 control chromosomes in the GnomAD database, including 497 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 0.066 (497 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 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: 0.0665 AC: 10113 AN: 152092 Hom.: 497 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.0236

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0424

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0314

Gnomad OTH AF: 0.0607

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

GnomAD4 genome AF: 0.0665 AC: 10117 AN: 152210 Hom.: 497 Cov.: 32 AF XY: 0.0675 AC XY: 5025 AN XY: 74432

African (AFR) AF: 0.110 AC: 4561 AN: 41530

American (AMR) AF: 0.0699 AC: 1070 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0236 AC: 82 AN: 3470

East Asian (EAS) AF: 0.207 AC: 1062 AN: 5128

South Asian (SAS) AF: 0.117 AC: 564 AN: 4818

European-Finnish (FIN) AF: 0.0424 AC: 450 AN: 10620

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0314 AC: 2135 AN: 68016

Other (OTH) AF: 0.0634 AC: 134 AN: 2114

Alfa AF: 0.0240 Hom.: 23

Bravo AF: 0.0722

Asia WGS AF: 0.172 AC: 600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.3
DANN	Benign	0.70
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10063995; hg19: chr5-174872204;