rs16949516

chr15-94775538-T-C

Variant summary

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

The XR_932644.3(LOC105370988):n.364-9521A>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 0.143 in 152,110 control chromosomes in the GnomAD database, including 3,254 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 0.14 (3254 hom., cov: 33)
• Consequence: LOC105370988 XR_932644.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70

Genes affected

LOC105370988 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370988	XR_932644.3	n.364-9521A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21643 AN: 151992 Hom.: 3244 Cov.: 33

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.0958

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.0473

Gnomad SAS AF: 0.0503

Gnomad FIN AF: 0.00867

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0442

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.143 AC: 21678 AN: 152110 Hom.: 3254 Cov.: 33 AF XY: 0.139 AC XY: 10329 AN XY: 74368

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.0956

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.0471

Gnomad4 SAS AF: 0.0497

Gnomad4 FIN AF: 0.00867

Gnomad4 NFE AF: 0.0442

Gnomad4 OTH AF: 0.127

Alfa AF: 0.0878 Hom.: 317

Bravo AF: 0.160

Asia WGS AF: 0.0800 AC: 277 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	0.034
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16949516; hg19: chr15-95318767;