chr2-138061031-T-C

Position:

• chr2-138061031-T-C

Variant summary

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

The XR_923367.2(LOC105373636):​n.804A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 151,980 control chromosomes in the GnomAD database, including 26,833 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 0.59 (26833 hom., cov: 32)
• Consequence: LOC105373636 XR_923367.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191

Genes affected

LOC105373636 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373636	XR_923367.2	n.804A>G		non_coding_transcript_exon_variant	1/3
LOC105373636	XR_923366.2	n.804A>G		non_coding_transcript_exon_variant	1/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90121 AN: 151862 Hom.: 26805 Cov.: 32

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.594 AC: 90203 AN: 151980 Hom.: 26833 Cov.: 32 AF XY: 0.592 AC XY: 43950 AN XY: 74296

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.674

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.608

Alfa AF: 0.591 Hom.: 4484

Bravo AF: 0.600

Asia WGS AF: 0.572 AC: 1987 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.2
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1996872; hg19: chr2-138818601;