rs2470644

Variant names:

• chr3-5735170-T-C
• rs2470644
• ENST00000425894.2:n.292-8494T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-5735170-T-C
• chr3-5735170-T-G

Variant summary

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

The ENST00000425894.2(ENSG00000229642):​n.292-8494T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,164 control chromosomes in the GnomAD database, including 8,454 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 (8454 hom., cov: 32)
• Consequence: ENSG00000229642 ENST00000425894.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 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.292-8494T>C		intron_variant	Intron 2 of 8	3
ENSG00000229642	ENST00000779001.1	n.212+38684T>C		intron_variant	Intron 2 of 7
ENSG00000229642	ENST00000779002.1	n.232+38684T>C		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34148 AN: 152044 Hom.: 8410 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0926

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.0376

Gnomad FIN AF: 0.0533

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0587

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.225 AC: 34257 AN: 152164 Hom.: 8454 Cov.: 32 AF XY: 0.219 AC XY: 16313 AN XY: 74418

African (AFR) AF: 0.617 AC: 25586 AN: 41442

American (AMR) AF: 0.140 AC: 2146 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0926 AC: 321 AN: 3468

East Asian (EAS) AF: 0.179 AC: 928 AN: 5184

South Asian (SAS) AF: 0.0373 AC: 180 AN: 4832

European-Finnish (FIN) AF: 0.0533 AC: 566 AN: 10614

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

European-Non Finnish (NFE) AF: 0.0587 AC: 3990 AN: 68016

Other (OTH) AF: 0.200 AC: 423 AN: 2110

Alfa AF: 0.112 Hom.: 3434

Bravo AF: 0.254

Asia WGS AF: 0.158 AC: 550 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	0.68
DANN	Benign	0.52
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2470644; hg19: chr3-5776857;