rs17580037

Positions:

• chr4-38139618-A-G
• chr4-38139618-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0942 in 152,232 control chromosomes in the GnomAD database, including 996 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 0.094 (996 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.404

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0942 AC: 14333 AN: 152114 Hom.: 994 Cov.: 32

Gnomad AFR AF: 0.0210

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.0730

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.0942 AC: 14341 AN: 152232 Hom.: 996 Cov.: 32 AF XY: 0.0946 AC XY: 7040 AN XY: 74446

Gnomad4 AFR AF: 0.0209

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.0730

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.118

Alfa AF: 0.113 Hom.: 490

Bravo AF: 0.0941

Asia WGS AF: 0.263 AC: 912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17580037; hg19: chr4-38141239;