5-151020073-T-C

Variant names:

• chr5-151020073-T-C
• rs8177406

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 0.149 in 152,198 control chromosomes in the GnomAD database, including 1,798 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 0.15 (1798 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.422
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 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: 0.149 AC: 22667 AN: 152078 Hom.: 1794 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.0954

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.149 AC: 22697 AN: 152198 Hom.: 1798 Cov.: 32 AF XY: 0.146 AC XY: 10852 AN XY: 74428

African (AFR) AF: 0.206 AC: 8568 AN: 41492

American (AMR) AF: 0.0952 AC: 1456 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 448 AN: 3472

East Asian (EAS) AF: 0.152 AC: 786 AN: 5180

South Asian (SAS) AF: 0.150 AC: 723 AN: 4826

European-Finnish (FIN) AF: 0.105 AC: 1116 AN: 10616

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9026 AN: 68008

Other (OTH) AF: 0.136 AC: 287 AN: 2106

Alfa AF: 0.134 Hom.: 2050

Bravo AF: 0.149

Asia WGS AF: 0.139 AC: 486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.8
DANN	Benign	0.60
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs8177406; hg19: chr5-150399634;