2-118080705-A-G

Position:

• chr2-118080705-A-G

Variant summary

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

The XR_001739662.3(LOC107985940):​n.181+7546T>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 0.626 in 152,066 control chromosomes in the GnomAD database, including 29,908 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 0.63 (29908 hom., cov: 32)
• Consequence: LOC107985940 XR_001739662.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327

Genes affected

LOC107985940 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985940	XR_001739662.3	n.181+7546T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.625 AC: 95035 AN: 151948 Hom.: 29874 Cov.: 32

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.626 AC: 95124 AN: 152066 Hom.: 29908 Cov.: 32 AF XY: 0.627 AC XY: 46647 AN XY: 74344

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.639

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.593

Alfa AF: 0.591 Hom.: 53108

Bravo AF: 0.625

Asia WGS AF: 0.652 AC: 2269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.77
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2161830; hg19: chr2-118838281; COSMIC: COSV60100142;