chr5-175426567-G-A

Variant names:

• chr5-175426567-G-A
• rs266001

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 0.14 in 152,080 control chromosomes in the GnomAD database, including 1,704 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 0.14 (1704 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 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: 0.140 AC: 21298 AN: 151962 Hom.: 1700 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.0899

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.140 AC: 21324 AN: 152080 Hom.: 1704 Cov.: 32 AF XY: 0.139 AC XY: 10354 AN XY: 74378

African (AFR) AF: 0.209 AC: 8688 AN: 41472

American (AMR) AF: 0.0897 AC: 1369 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3470

East Asian (EAS) AF: 0.105 AC: 546 AN: 5176

South Asian (SAS) AF: 0.109 AC: 526 AN: 4826

European-Finnish (FIN) AF: 0.119 AC: 1259 AN: 10584

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.118 AC: 8053 AN: 67970

Other (OTH) AF: 0.124 AC: 261 AN: 2112

Alfa AF: 0.130 Hom.: 722

Bravo AF: 0.143

Asia WGS AF: 0.118 AC: 409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	10
DANN	Benign	0.93
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs266001; hg19: chr5-174853570; COSMIC: COSV60236591;