rs4667682

Positions:

• chr2-171271410-C-T

Variant summary

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

The XR_923573.3(LOC105373737):​n.130-68G>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 0.166 in 152,188 control chromosomes in the GnomAD database, including 2,782 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 0.17 (2782 hom., cov: 32)
• Consequence: LOC105373737 XR_923573.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257

Genes affected

LOC105373737 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373737	XR_923573.3	n.130-68G>A		intron_variant, non_coding_transcript_variant
LOC105373737	XR_007087295.1	n.3547-68G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25280 AN: 152070 Hom.: 2777 Cov.: 32

Gnomad AFR AF: 0.0703

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.166 AC: 25295 AN: 152188 Hom.: 2782 Cov.: 32 AF XY: 0.175 AC XY: 13053 AN XY: 74412

Gnomad4 AFR AF: 0.0703

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.197

Alfa AF: 0.165 Hom.: 4537

Bravo AF: 0.168

Asia WGS AF: 0.285 AC: 993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.0
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4667682; hg19: chr2-172127920; COSMIC: COSV69716549;