2-104119794-C-G

Position:

• chr2-104119794-C-G

Variant summary

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

The XR_923128.1(LOC105373523):​n.538-4508G>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 0.123 in 152,032 control chromosomes in the GnomAD database, including 1,984 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 0.12 (1984 hom., cov: 33)
• Consequence: LOC105373523 XR_923128.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260

Genes affected

LOC105373523 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373523	XR_923128.1	n.538-4508G>C		intron_variant, non_coding_transcript_variant
LOC105373523	XR_923127.1	n.542-4508G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18640 AN: 151912 Hom.: 1983 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.0602

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.0993

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

GnomAD4 genome AF: 0.123 AC: 18648 AN: 152032 Hom.: 1984 Cov.: 33 AF XY: 0.127 AC XY: 9455 AN XY: 74286

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.0646

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.0602

Gnomad4 NFE AF: 0.0415

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0187 Hom.: 18

Bravo AF: 0.137

Asia WGS AF: 0.283 AC: 981 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.5
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10189155; hg19: chr2-104736252;