rs1915501

Variant names:

• chr4-28934741-A-G
• rs1915501

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;