rs4350528

Positions:

• chr15-93620471-G-A
• chr15-93620471-G-T

Variant summary

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

The XR_001751681.2(LOC107983974):​n.1032+27738G>A 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 0.523 in 151,970 control chromosomes in the GnomAD database, including 25,874 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 0.52 (25874 hom., cov: 32)
• Consequence: LOC107983974 XR_001751681.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

LOC107983974 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107983974	XR_001751681.2	n.1032+27738G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000554318.2	n.324+27112G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000653322.2	n.964+27738G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79480 AN: 151852 Hom.: 25868 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.523 AC: 79496 AN: 151970 Hom.: 25874 Cov.: 32 AF XY: 0.516 AC XY: 38350 AN XY: 74274

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.586

Alfa AF: 0.698 Hom.: 66735

Bravo AF: 0.509

Asia WGS AF: 0.456 AC: 1589 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	0.84
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4350528; hg19: chr15-94163700;