2-195009522-T-C

Variant names:

• chr2-195009522-T-C
• rs12472928
• ENST00000418387.1:n.147-4930A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007088699.1(LOC105376755):​n.265+49913A>G variant causes a intron 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: LOC105376755 XR_007088699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 3 publications found

Genes affected

ENSG00000235056 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418387.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000235056	ENST00000418387.1	TSL:5	n.147-4930A>G		intron	N/A

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

African (AFR) AF: 0.235 AC: 9745 AN: 41382

American (AMR) AF: 0.707 AC: 10720 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2447 AN: 3454

East Asian (EAS) AF: 0.551 AC: 2811 AN: 5104

South Asian (SAS) AF: 0.599 AC: 2884 AN: 4818

European-Finnish (FIN) AF: 0.619 AC: 6541 AN: 10570

Middle Eastern (MID) AF: 0.714 AC: 207 AN: 290

European-Non Finnish (NFE) AF: 0.675 AC: 45504 AN: 67456

Other (OTH) AF: 0.591 AC: 1239 AN: 2098

Alfa AF: 0.574 Hom.: 5246

Bravo AF: 0.539

Asia WGS AF: 0.533 AC: 1853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.57
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs12472928; hg19: chr2-195874246;