5-151020289-A-T

Variant names:

• chr5-151020289-A-T
• rs8177409

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 0.137 in 281,296 control chromosomes in the GnomAD database, including 2,797 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 (1787 hom., cov: 33)
  • Exomes 𝑓: 0.12 (1010 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 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: 0.148 AC: 22584 AN: 152170 Hom.: 1785 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.0951

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.139

GnomAD4 exome AF: 0.123 AC: 15817 AN: 129008 Hom.: 1010 AF XY: 0.124 AC XY: 8098 AN XY: 65446

African (AFR) AF: 0.207 AC: 853 AN: 4118

American (AMR) AF: 0.0807 AC: 285 AN: 3532

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 675 AN: 5038

East Asian (EAS) AF: 0.119 AC: 1140 AN: 9588

South Asian (SAS) AF: 0.123 AC: 550 AN: 4476

European-Finnish (FIN) AF: 0.0997 AC: 1097 AN: 10998

Middle Eastern (MID) AF: 0.180 AC: 127 AN: 704

European-Non Finnish (NFE) AF: 0.122 AC: 9959 AN: 81700

Other (OTH) AF: 0.128 AC: 1131 AN: 8854

GnomAD4 genome AF: 0.148 AC: 22608 AN: 152288 Hom.: 1787 Cov.: 33 AF XY: 0.145 AC XY: 10806 AN XY: 74464

African (AFR) AF: 0.204 AC: 8466 AN: 41542

American (AMR) AF: 0.0949 AC: 1453 AN: 15310

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

East Asian (EAS) AF: 0.152 AC: 787 AN: 5184

South Asian (SAS) AF: 0.150 AC: 726 AN: 4830

European-Finnish (FIN) AF: 0.106 AC: 1121 AN: 10614

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

European-Non Finnish (NFE) AF: 0.133 AC: 9030 AN: 68018

Other (OTH) AF: 0.137 AC: 290 AN: 2114

Alfa AF: 0.0666 Hom.: 80

Bravo AF: 0.148

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	-0.94
CADD	Benign	2.7
DANN	Benign	0.77
PhyloP100		-0.22
PromoterAI		-0.039	Neutral

Splicing

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

Other links and lift over

dbSNP: rs8177409; hg19: chr5-150399850;