rs148915469

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000506494.1(ENSG00000250300):​n.243-2395T>G variant causes a intron, non coding transcript 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: ENST00000506494.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 107 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000506494.1	n.243-2395T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.00462

Gnomad4 AMR AF: 0.0420

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00559

Gnomad4 FIN AF: 0.0143

Gnomad4 NFE AF: 0.0261

Gnomad4 OTH AF: 0.0473

Alfa AF: 0.0120 Hom.: 2

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs148915469; hg19: chr4-100395414;