rs4775913

Variant names:

• chr15-51027237-G-A
• rs4775913

Your query was ambiguous. Multiple possible variants found:

• chr15-51027237-G-A
• chr15-51027237-G-C

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 0.209 in 151,506 control chromosomes in the GnomAD database, including 3,454 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 0.21 (3454 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 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: 0.209 AC: 31703 AN: 151390 Hom.: 3457 Cov.: 30

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.209 AC: 31705 AN: 151506 Hom.: 3454 Cov.: 30 AF XY: 0.214 AC XY: 15851 AN XY: 73972

African (AFR) AF: 0.134 AC: 5528 AN: 41312

American (AMR) AF: 0.251 AC: 3826 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 510 AN: 3462

East Asian (EAS) AF: 0.396 AC: 2032 AN: 5126

South Asian (SAS) AF: 0.268 AC: 1279 AN: 4768

European-Finnish (FIN) AF: 0.296 AC: 3086 AN: 10434

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.217 AC: 14740 AN: 67878

Other (OTH) AF: 0.198 AC: 417 AN: 2102

Alfa AF: 0.120 Hom.: 179

Bravo AF: 0.206

Asia WGS AF: 0.335 AC: 1166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.1
DANN	Benign	0.50
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs4775913; hg19: chr15-51319434;