chr2-139246243-G-C

Position:

• chr2-139246243-G-C

Variant summary

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

The XR_001739720.2(LOC105373643):​n.116+11455G>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 0.135 in 152,180 control chromosomes in the GnomAD database, including 1,488 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 0.14 (1488 hom., cov: 32)
• Consequence: LOC105373643 XR_001739720.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.709

Genes affected

LOC105373643 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373643	XR_001739720.2	n.116+11455G>C		intron_variant, non_coding_transcript_variant
LOC105373643	XR_001739721.2	n.103+11455G>C		intron_variant, non_coding_transcript_variant
LOC105373643	XR_923373.3	n.103+11455G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20568 AN: 152062 Hom.: 1487 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0669

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.135 AC: 20574 AN: 152180 Hom.: 1488 Cov.: 32 AF XY: 0.131 AC XY: 9780 AN XY: 74400

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.0669

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.128

Alfa AF: 0.128 Hom.: 164

Bravo AF: 0.138

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13419861; hg19: chr2-140003813;