2-195009522-T-C

Position:

• chr2-195009522-T-C

Variant summary

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

The ENST00000418387.1(ENSG00000235056):​n.147-4930A>G 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 0.547 in 151,244 control chromosomes in the GnomAD database, including 25,602 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 0.55 (25602 hom., cov: 33)
• Consequence: ENST00000418387.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376755	XR_007088699.1	n.265+49913A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000418387.1	n.147-4930A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.547 AC: 82720 AN: 151124 Hom.: 25601 Cov.: 33

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.702

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.547 AC: 82733 AN: 151244 Hom.: 25602 Cov.: 33 AF XY: 0.549 AC XY: 40547 AN XY: 73872

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.591

Alfa AF: 0.583 Hom.: 5215

Bravo AF: 0.539

Asia WGS AF: 0.533 AC: 1853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
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: rs12472928; hg19: chr2-195874246;