rs1034200

Variant names:

• chr13-22654552-C-A
• rs1034200
• ENST00000815334.1:n.440-2792G>T

Your query was ambiguous. Multiple possible variants found:

• chr13-22654552-C-A
• chr13-22654552-C-T

Variant summary

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

The ENST00000815334.1(ENSG00000306102):​n.440-2792G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,994 control chromosomes in the GnomAD database, including 12,618 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 0.38 (12618 hom., cov: 32)
• Consequence: ENSG00000306102 ENST00000815334.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 27 publications found

Genes affected

ENSG00000306102 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306102	ENST00000815334.1	n.440-2792G>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58005 AN: 151874 Hom.: 12595 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.382 AC: 58076 AN: 151994 Hom.: 12618 Cov.: 32 AF XY: 0.382 AC XY: 28371 AN XY: 74290

African (AFR) AF: 0.598 AC: 24796 AN: 41436

American (AMR) AF: 0.300 AC: 4583 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 870 AN: 3472

East Asian (EAS) AF: 0.334 AC: 1728 AN: 5174

South Asian (SAS) AF: 0.213 AC: 1025 AN: 4814

European-Finnish (FIN) AF: 0.413 AC: 4359 AN: 10546

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19667 AN: 67966

Other (OTH) AF: 0.357 AC: 753 AN: 2110

Alfa AF: 0.307 Hom.: 34868

Bravo AF: 0.382

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.46
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs1034200; hg19: chr13-23228691;