chr15-97086204-C-T

Position:

• chr15-97086204-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_932683.2(LOC105371004):​n.258-2936G>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 0.0428 in 152,030 control chromosomes in the GnomAD database, including 160 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 0.043 (160 hom., cov: 32)
• Consequence: LOC105371004 XR_932683.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.615

Genes affected

LOC105371004 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0428 (6514/152030) while in subpopulation NFE AF= 0.0462 (3138/67982). AF 95% confidence interval is 0.0448. There are 160 homozygotes in gnomad4. There are 3035 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 160 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371004	XR_932683.2	n.258-2936G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0427 AC: 6489 AN: 151912 Hom.: 153 Cov.: 32

Gnomad AFR AF: 0.0442

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0356

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.0433

Gnomad SAS AF: 0.0453

Gnomad FIN AF: 0.0312

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0462

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0428 AC: 6514 AN: 152030 Hom.: 160 Cov.: 32 AF XY: 0.0408 AC XY: 3035 AN XY: 74328

Gnomad4 AFR AF: 0.0446

Gnomad4 AMR AF: 0.0354

Gnomad4 ASJ AF: 0.0248

Gnomad4 EAS AF: 0.0434

Gnomad4 SAS AF: 0.0458

Gnomad4 FIN AF: 0.0312

Gnomad4 NFE AF: 0.0462

Gnomad4 OTH AF: 0.0445

Alfa AF: 0.0448 Hom.: 219

Bravo AF: 0.0432

Asia WGS AF: 0.0670 AC: 232 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	14
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11852342; hg19: chr15-97629434;