rs2470646

Variant names:

• chr3-5734078-T-C
• rs2470646
• ENST00000425894.2:n.292-9586T>C

Variant summary

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

The ENST00000425894.2(ENSG00000229642):​n.292-9586T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,118 control chromosomes in the GnomAD database, including 8,419 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 0.23 (8419 hom., cov: 32)
• Consequence: ENSG00000229642 ENST00000425894.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444
• Publications: 1 publications found

Genes affected

ENSG00000229642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.609 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
ENSG00000229642	ENST00000425894.2	n.292-9586T>C		intron_variant	Intron 2 of 8	3
ENSG00000229642	ENST00000779001.1	n.212+37592T>C		intron_variant	Intron 2 of 7
ENSG00000229642	ENST00000779002.1	n.232+37592T>C		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34243 AN: 152000 Hom.: 8374 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0950

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.0398

Gnomad FIN AF: 0.0602

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0599

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.226 AC: 34355 AN: 152118 Hom.: 8419 Cov.: 32 AF XY: 0.220 AC XY: 16362 AN XY: 74378

African (AFR) AF: 0.616 AC: 25515 AN: 41436

American (AMR) AF: 0.140 AC: 2149 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0950 AC: 329 AN: 3464

East Asian (EAS) AF: 0.178 AC: 918 AN: 5168

South Asian (SAS) AF: 0.0394 AC: 190 AN: 4824

European-Finnish (FIN) AF: 0.0602 AC: 639 AN: 10612

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0599 AC: 4070 AN: 68000

Other (OTH) AF: 0.203 AC: 429 AN: 2112

Alfa AF: 0.184 Hom.: 952

Bravo AF: 0.254

Asia WGS AF: 0.165 AC: 576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.26
DANN	Benign	0.47
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs2470646; hg19: chr3-5775765;