rs148915469

Variant names:

• chr4-99474257-A-C
• rs148915469
• ENST00000506494.1:n.243-2395T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-99474257-A-C
• chr4-99474257-A-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000506494.1(ENSG00000250300):​n.243-2395T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0229 in 152,318 control chromosomes in the GnomAD database, including 107 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 0.023 (107 hom., cov: 32)
• Consequence: ENSG00000250300 ENST00000506494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 3 publications found

Genes affected

ENSG00000250300 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0229 (3491/152318) while in subpopulation AMR AF = 0.042 (643/15292). AF 95% confidence interval is 0.0394. There are 107 homozygotes in GnomAd4. There are 1712 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 107 gene

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
ENSG00000250300	ENST00000506494.1	n.243-2395T>G		intron_variant	Intron 2 of 3	6

Frequencies

GnomAD3 genomes AF: 0.0230 AC: 3496 AN: 152200 Hom.: 107 Cov.: 32

Gnomad AFR AF: 0.00463

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0422

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00579

Gnomad FIN AF: 0.0143

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0261

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0229 AC: 3491 AN: 152318 Hom.: 107 Cov.: 32 AF XY: 0.0230 AC XY: 1712 AN XY: 74490

African (AFR) AF: 0.00462 AC: 192 AN: 41576

American (AMR) AF: 0.0420 AC: 643 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.00559 AC: 27 AN: 4828

European-Finnish (FIN) AF: 0.0143 AC: 152 AN: 10622

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0261 AC: 1777 AN: 68026

Other (OTH) AF: 0.0473 AC: 100 AN: 2114

Alfa AF: 0.0145 Hom.: 14

Bravo AF: 0.0249

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.39
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs148915469; hg19: chr4-100395414;