rs3100717

chr2-138016981-C-T

Variant summary

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

The XR_001739719.2(LOC107985948):n.239-9185G>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 0.315 in 151,952 control chromosomes in the GnomAD database, including 9,020 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 0.31 (9020 hom., cov: 32)
• Consequence: LOC107985948 XR_001739719.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

Genes affected

LOC107985948 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985948	XR_001739719.2	n.239-9185G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47756 AN: 151832 Hom.: 8996 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.315 AC: 47848 AN: 151952 Hom.: 9020 Cov.: 32 AF XY: 0.318 AC XY: 23585 AN XY: 74268

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.314

Alfa AF: 0.277 Hom.: 1123

Bravo AF: 0.329

Asia WGS AF: 0.352 AC: 1221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.9
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3100717; hg19: chr2-138774551;