rs1914650

Positions:

• chr2-155780197-G-A

Variant summary

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

The XR_007088689.1(LOC105373703):​n.896-20472C>T 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 0.182 in 151,650 control chromosomes in the GnomAD database, including 3,156 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 0.18 (3156 hom., cov: 32)
• Consequence: LOC105373703 XR_007088689.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

LOC105373703 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373703	XR_007088689.1	n.896-20472C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27636 AN: 151530 Hom.: 3159 Cov.: 32

Gnomad AFR AF: 0.0594

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.0473

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.298

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.182 AC: 27629 AN: 151650 Hom.: 3156 Cov.: 32 AF XY: 0.177 AC XY: 13129 AN XY: 74130

Gnomad4 AFR AF: 0.0593

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.0470

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.196

Alfa AF: 0.239 Hom.: 2572

Bravo AF: 0.173

Asia WGS AF: 0.0940 AC: 329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.10
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1914650; hg19: chr2-156636709;