rs17580037

Variant names:

• chr4-38139618-A-G
• rs17580037

Your query was ambiguous. Multiple possible variants found:

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

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 0.0942 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0209 AC: 869 AN: 41570

American (AMR) AF: 0.100 AC: 1531 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 627 AN: 3470

East Asian (EAS) AF: 0.308 AC: 1592 AN: 5162

South Asian (SAS) AF: 0.208 AC: 1003 AN: 4816

European-Finnish (FIN) AF: 0.0730 AC: 774 AN: 10606

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7613 AN: 68006

Other (OTH) AF: 0.118 AC: 248 AN: 2106

Alfa AF: 0.110 Hom.: 621

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
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs17580037; hg19: chr4-38141239;