5-121634753-A-G

Variant names:

• chr5-121634753-A-G
• rs1508805

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 0.667 in 152,126 control chromosomes in the GnomAD database, including 34,602 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 0.67 (34602 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 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: 0.667 AC: 101459 AN: 152008 Hom.: 34592 Cov.: 34

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.667 AC: 101504 AN: 152126 Hom.: 34602 Cov.: 34 AF XY: 0.667 AC XY: 49590 AN XY: 74358

African (AFR) AF: 0.514 AC: 21351 AN: 41510

American (AMR) AF: 0.742 AC: 11340 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2437 AN: 3466

East Asian (EAS) AF: 0.780 AC: 4043 AN: 5182

South Asian (SAS) AF: 0.769 AC: 3714 AN: 4828

European-Finnish (FIN) AF: 0.678 AC: 7175 AN: 10578

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.724 AC: 49228 AN: 67970

Other (OTH) AF: 0.675 AC: 1426 AN: 2112

Alfa AF: 0.714 Hom.: 63630

Bravo AF: 0.667

Asia WGS AF: 0.706 AC: 2447 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.49
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs1508805; hg19: chr5-120970448;