rs1504501

Variant names:

• chr4-45959387-A-G
• rs1504501
• ENST00000794649.1:n.337-1353T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000794649.1(ENSG00000303444):​n.337-1353T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,116 control chromosomes in the GnomAD database, including 3,291 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 0.19 (3291 hom., cov: 32)
• Consequence: ENSG00000303444 ENST00000794649.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.479
• Publications: 7 publications found

Genes affected

ENSG00000303444 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 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
ENSG00000303444	ENST00000794649.1	n.337-1353T>C		intron_variant	Intron 3 of 3
ENSG00000303444	ENST00000794650.1	n.207-1353T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29377 AN: 151996 Hom.: 3298 Cov.: 32

Gnomad AFR AF: 0.0915

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.193 AC: 29361 AN: 152116 Hom.: 3291 Cov.: 32 AF XY: 0.194 AC XY: 14392 AN XY: 74352

African (AFR) AF: 0.0912 AC: 3789 AN: 41532

American (AMR) AF: 0.220 AC: 3359 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1233 AN: 3470

East Asian (EAS) AF: 0.354 AC: 1834 AN: 5176

South Asian (SAS) AF: 0.235 AC: 1134 AN: 4832

European-Finnish (FIN) AF: 0.211 AC: 2233 AN: 10588

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15132 AN: 67944

Other (OTH) AF: 0.219 AC: 462 AN: 2110

Alfa AF: 0.215 Hom.: 2330

Bravo AF: 0.191

Asia WGS AF: 0.283 AC: 983 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.9
DANN	Benign	0.21
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs1504501; hg19: chr4-45961404;