5-85287951-G-T

Variant names:

• chr5-85287951-G-T
• rs12153606

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 0.131 in 152,096 control chromosomes in the GnomAD database, including 1,666 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 0.13 (1666 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 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: 0.131 AC: 19909 AN: 151978 Hom.: 1665 Cov.: 32

Gnomad AFR AF: 0.0438

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.131 AC: 19927 AN: 152096 Hom.: 1666 Cov.: 32 AF XY: 0.128 AC XY: 9517 AN XY: 74334

African (AFR) AF: 0.0439 AC: 1825 AN: 41540

American (AMR) AF: 0.116 AC: 1767 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 598 AN: 3470

East Asian (EAS) AF: 0.0110 AC: 57 AN: 5176

South Asian (SAS) AF: 0.125 AC: 603 AN: 4828

European-Finnish (FIN) AF: 0.154 AC: 1626 AN: 10566

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13018 AN: 67922

Other (OTH) AF: 0.144 AC: 305 AN: 2112

Alfa AF: 0.154 Hom.: 261

Bravo AF: 0.124

Asia WGS AF: 0.0860 AC: 301 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.67
DANN	Benign	0.62
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs12153606; hg19: chr5-84583769; COSMIC: COSV51332599;