rs37008

Variant names:

• chr5-1351423-G-A
• rs37008

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 0.446 in 152,064 control chromosomes in the GnomAD database, including 15,949 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 0.45 (15949 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 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: 0.446 AC: 67722 AN: 151946 Hom.: 15932 Cov.: 33

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.446 AC: 67786 AN: 152064 Hom.: 15949 Cov.: 33 AF XY: 0.437 AC XY: 32470 AN XY: 74322

African (AFR) AF: 0.576 AC: 23877 AN: 41458

American (AMR) AF: 0.341 AC: 5216 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1452 AN: 3472

East Asian (EAS) AF: 0.177 AC: 918 AN: 5172

South Asian (SAS) AF: 0.203 AC: 977 AN: 4818

European-Finnish (FIN) AF: 0.434 AC: 4588 AN: 10564

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29250 AN: 67974

Other (OTH) AF: 0.429 AC: 906 AN: 2110

Alfa AF: 0.431 Hom.: 6421

Bravo AF: 0.449

Asia WGS AF: 0.229 AC: 799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.42
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs37008; hg19: chr5-1351538;