rs2199734

chr15-94773214-C-T

Variant summary

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

The XR_932644.3(LOC105370988):n.364-7197G>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 0.773 in 152,120 control chromosomes in the GnomAD database, including 45,902 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 0.77 (45902 hom., cov: 32)
• Consequence: LOC105370988 XR_932644.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

Genes affected

LOC105370988 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370988	XR_932644.3	n.364-7197G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117500 AN: 152002 Hom.: 45840 Cov.: 32

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.773 AC: 117624 AN: 152120 Hom.: 45902 Cov.: 32 AF XY: 0.767 AC XY: 57028 AN XY: 74324

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.805

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.739

Gnomad4 OTH AF: 0.760

Alfa AF: 0.741 Hom.: 56358

Bravo AF: 0.779

Asia WGS AF: 0.729 AC: 2536 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	0.17
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2199734; hg19: chr15-95316443;