rs1504749

Variant names:

• chr8-54398151-A-C
• rs1504749

Your query was ambiguous. Multiple possible variants found:

• chr8-54398151-A-C
• chr8-54398151-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 0.3 in 151,982 control chromosomes in the GnomAD database, including 7,640 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 0.30 (7640 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 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: 0.300 AC: 45531 AN: 151864 Hom.: 7625 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.300 AC: 45596 AN: 151982 Hom.: 7640 Cov.: 32 AF XY: 0.304 AC XY: 22550 AN XY: 74278

African (AFR) AF: 0.430 AC: 17809 AN: 41432

American (AMR) AF: 0.390 AC: 5950 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 595 AN: 3470

East Asian (EAS) AF: 0.331 AC: 1708 AN: 5162

South Asian (SAS) AF: 0.380 AC: 1828 AN: 4812

European-Finnish (FIN) AF: 0.241 AC: 2546 AN: 10552

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14346 AN: 67974

Other (OTH) AF: 0.283 AC: 598 AN: 2114

Alfa AF: 0.244 Hom.: 12653

Bravo AF: 0.316

Asia WGS AF: 0.380 AC: 1322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.93
DANN	Benign	0.54
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1504749; hg19: chr8-55310711;