rs2444728

Positions:

• chr15-36457229-A-C
• chr15-36457229-A-G
• chr15-36457229-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558875.1(ENSG00000259737):​n.205+11650T>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 0.925 in 152,070 control chromosomes in the GnomAD database, including 65,440 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 0.92 (65440 hom., cov: 31)
• Consequence: ENST00000558875.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370768	XR_932110.1	n.248+6016A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000558875.1	n.205+11650T>G		intron_variant, non_coding_transcript_variant		3
	ENST00000558262.5	n.122+3099T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.925 AC: 140566 AN: 151952 Hom.: 65400 Cov.: 31

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.945

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

GnomAD4 genome AF: 0.925 AC: 140661 AN: 152070 Hom.: 65440 Cov.: 31 AF XY: 0.924 AC XY: 68709 AN XY: 74346

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.937

Gnomad4 ASJ AF: 0.960

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.911

Gnomad4 FIN AF: 0.978

Gnomad4 NFE AF: 0.982

Gnomad4 OTH AF: 0.945

Alfa AF: 0.969 Hom.: 78162

Bravo AF: 0.914

Asia WGS AF: 0.903 AC: 3141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2444728; hg19: chr15-36749430;