rs17074631

chr4-183356154-A-G

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 0.105 in 152,170 control chromosomes in the GnomAD database, including 919 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 0.10 (919 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 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: 0.105 AC: 15897 AN: 152052 Hom.: 914 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.0703

Gnomad ASJ AF: 0.0291

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.0492

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0981

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

GnomAD4 genome AF: 0.105 AC: 15928 AN: 152170 Hom.: 919 Cov.: 32 AF XY: 0.103 AC XY: 7685 AN XY: 74396

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.0705

Gnomad4 ASJ AF: 0.0291

Gnomad4 EAS AF: 0.0110

Gnomad4 SAS AF: 0.0490

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.0980

Alfa AF: 0.106 Hom.: 1154

Bravo AF: 0.0985

Asia WGS AF: 0.0480 AC: 167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.2
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17074631; hg19: chr4-184277307;