rs9341234

Variant names:

• chr2-216665825-T-C
• rs9341234
• ENST00000735028.1:n.265+447T>C

Variant summary

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

The ENST00000735028.1(ENSG00000296004):​n.265+447T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,202 control chromosomes in the GnomAD database, including 1,413 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 0.10 (1413 hom., cov: 33)
• Consequence: ENSG00000296004 ENST00000735028.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495
• Publications: 4 publications found

Genes affected

ENSG00000296004 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 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
ENSG00000296004	ENST00000735028.1	n.265+447T>C		intron_variant	Intron 1 of 1
ENSG00000296004	ENST00000735029.1	n.255+447T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15226 AN: 152084 Hom.: 1394 Cov.: 33

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0637

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.0789

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0249

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0361

Gnomad OTH AF: 0.0823

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

GnomAD4 genome AF: 0.100 AC: 15284 AN: 152202 Hom.: 1413 Cov.: 33 AF XY: 0.0987 AC XY: 7343 AN XY: 74416

African (AFR) AF: 0.247 AC: 10266 AN: 41492

American (AMR) AF: 0.0638 AC: 977 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3468

East Asian (EAS) AF: 0.0785 AC: 406 AN: 5170

South Asian (SAS) AF: 0.101 AC: 487 AN: 4818

European-Finnish (FIN) AF: 0.0249 AC: 265 AN: 10622

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0361 AC: 2455 AN: 68010

Other (OTH) AF: 0.0810 AC: 171 AN: 2112

Alfa AF: 0.0706 Hom.: 90

Bravo AF: 0.108

Asia WGS AF: 0.0920 AC: 318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.55
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs9341234; hg19: chr2-217530548;