rs4260001

Positions:

• chr15-93639633-C-G
• chr15-93639633-C-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+46900C>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 0.336 in 151,884 control chromosomes in the GnomAD database, including 9,080 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 0.34 (9080 hom., cov: 30)
• Consequence: LOC107983974 XR_001751681.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

LOC107983974 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107983974	XR_001751681.2	n.1032+46900C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000554318.2	n.324+46274C>G		intron_variant, non_coding_transcript_variant		3
	ENST00000653322.2	n.965-16681C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.336 AC: 50948 AN: 151766 Hom.: 9069 Cov.: 30

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.336 AC: 50989 AN: 151884 Hom.: 9080 Cov.: 30 AF XY: 0.351 AC XY: 26061 AN XY: 74228

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.333

Alfa AF: 0.171 Hom.: 337

Bravo AF: 0.328

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.31
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4260001; hg19: chr15-94182862;