chr5-95318169-G-A

Variant names:

• chr5-95318169-G-A
• rs255982

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 0.125 in 152,086 control chromosomes in the GnomAD database, including 1,395 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 0.12 (1395 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.471
• Publications: 5 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 (NFE) allele frequency at 95% confidence interval = 0.155 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: 0.125 AC: 19006 AN: 151968 Hom.: 1394 Cov.: 31

Gnomad AFR AF: 0.0493

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0411

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.125 AC: 19005 AN: 152086 Hom.: 1395 Cov.: 31 AF XY: 0.128 AC XY: 9511 AN XY: 74346

African (AFR) AF: 0.0492 AC: 2042 AN: 41512

American (AMR) AF: 0.150 AC: 2288 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 442 AN: 3470

East Asian (EAS) AF: 0.0412 AC: 213 AN: 5174

South Asian (SAS) AF: 0.124 AC: 597 AN: 4812

European-Finnish (FIN) AF: 0.215 AC: 2271 AN: 10562

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10699 AN: 67960

Other (OTH) AF: 0.132 AC: 280 AN: 2114

Alfa AF: 0.136 Hom.: 2714

Bravo AF: 0.115

Asia WGS AF: 0.0770 AC: 265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.9
DANN	Benign	0.37
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs255982; hg19: chr5-94653873;