rs16842314

chr2-139460790-G-A

Variant summary

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

The XR_923378.3(LOC105373645):n.616-8985G>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 0.0276 in 152,180 control chromosomes in the GnomAD database, including 145 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 0.028 (145 hom., cov: 32)
• Consequence: LOC105373645 XR_923378.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

Genes affected

LOC105373645 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373645	XR_923378.3	n.616-8985G>A		intron_variant, non_coding_transcript_variant
LOC105373645	XR_007088681.1	n.616-8985G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0276 AC: 4199 AN: 152062 Hom.: 142 Cov.: 32

Gnomad AFR AF: 0.00800

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0486

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.0523

Gnomad FIN AF: 0.0329

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.0215

Gnomad OTH AF: 0.0325

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

GnomAD4 genome AF: 0.0276 AC: 4199 AN: 152180 Hom.: 145 Cov.: 32 AF XY: 0.0303 AC XY: 2257 AN XY: 74380

Gnomad4 AFR AF: 0.00797

Gnomad4 AMR AF: 0.0486

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.0513

Gnomad4 FIN AF: 0.0329

Gnomad4 NFE AF: 0.0214

Gnomad4 OTH AF: 0.0355

Alfa AF: 0.0222 Hom.: 61

Bravo AF: 0.0290

Asia WGS AF: 0.121 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.0
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16842314; hg19: chr2-140218360;