rs1915501

chr4-28934741-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 0.28 in 152,060 control chromosomes in the GnomAD database, including 7,770 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 0.28 (7770 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 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: 0.280 AC: 42523 AN: 151942 Hom.: 7748 Cov.: 32

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0339

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.280 AC: 42601 AN: 152060 Hom.: 7770 Cov.: 32 AF XY: 0.280 AC XY: 20837 AN XY: 74348

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.0342

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.244

Alfa AF: 0.221 Hom.: 1728

Bravo AF: 0.292

Asia WGS AF: 0.154 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.68
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1915501; hg19: chr4-28936363;