rs16861690

Positions:

• chr2-173441809-A-G

Variant summary

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

The XR_923586.2(LOC105373744):​n.264-1445T>C 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 0.153 in 152,164 control chromosomes in the GnomAD database, including 2,899 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 0.15 (2899 hom., cov: 33)
• Consequence: LOC105373744 XR_923586.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

LOC105373744 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373744	XR_923586.2	n.264-1445T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23195 AN: 152046 Hom.: 2895 Cov.: 33

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.0463

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0879

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.0567

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0563

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.153 AC: 23223 AN: 152164 Hom.: 2899 Cov.: 33 AF XY: 0.153 AC XY: 11362 AN XY: 74400

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.0879

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.0567

Gnomad4 NFE AF: 0.0563

Gnomad4 OTH AF: 0.151

Alfa AF: 0.0766 Hom.: 1473

Bravo AF: 0.163

Asia WGS AF: 0.298 AC: 1032 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16861690; hg19: chr2-174306537;