15-73641377-A-G

Position:

• chr15-73641377-A-G

Variant summary

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

The XR_932451.3(LOC105370891):​n.321+4640A>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 0.0958 in 152,186 control chromosomes in the GnomAD database, including 889 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 0.096 (889 hom., cov: 32)
• Consequence: LOC105370891 XR_932451.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.12

Genes affected

LOC105370891 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370891	XR_932451.3	n.321+4640A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0956 AC: 14544 AN: 152068 Hom.: 883 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.0501

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0719

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0616

Gnomad OTH AF: 0.0803

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

GnomAD4 genome AF: 0.0958 AC: 14576 AN: 152186 Hom.: 889 Cov.: 32 AF XY: 0.0966 AC XY: 7185 AN XY: 74406

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.0775

Gnomad4 ASJ AF: 0.0501

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.0719

Gnomad4 NFE AF: 0.0616

Gnomad4 OTH AF: 0.0814

Alfa AF: 0.0667 Hom.: 841

Bravo AF: 0.0983

Asia WGS AF: 0.148 AC: 512 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.7
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1564492; hg19: chr15-73933718;