ENST00000438070.3:n.348-2504T>C

Variant names:

• chr2-206860892-T-C
• rs10192834
• ENST00000438070.3:n.348-2504T>C

Variant summary

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

The ENST00000438070.3(ENSG00000229321):​n.348-2504T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 151,974 control chromosomes in the GnomAD database, including 9,077 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 0.34 (9077 hom., cov: 30)
• Consequence: ENSG00000229321 ENST00000438070.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 4 publications found

Genes affected

ENSG00000229321 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438070.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229321	ENST00000438070.3	TSL:3	n.348-2504T>C		intron	N/A
	ENSG00000229321	ENST00000658291.1		n.3035-2504T>C		intron	N/A
	ENSG00000229321	ENST00000658889.1		n.2974-18491T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52129 AN: 151856 Hom.: 9072 Cov.: 30

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.343 AC: 52171 AN: 151974 Hom.: 9077 Cov.: 30 AF XY: 0.340 AC XY: 25223 AN XY: 74280

African (AFR) AF: 0.384 AC: 15918 AN: 41430

American (AMR) AF: 0.294 AC: 4491 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1354 AN: 3470

East Asian (EAS) AF: 0.318 AC: 1637 AN: 5144

South Asian (SAS) AF: 0.258 AC: 1243 AN: 4816

European-Finnish (FIN) AF: 0.315 AC: 3324 AN: 10560

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23121 AN: 67968

Other (OTH) AF: 0.375 AC: 790 AN: 2106

Alfa AF: 0.348 Hom.: 25594

Bravo AF: 0.347

Asia WGS AF: 0.280 AC: 976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.51
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10192834; hg19: chr2-207725616;