chr3-3304454-G-A

Variant names:

• chr3-3304454-G-A
• rs10510257
• ENST00000420000.6:n.537+32846C>T

Variant summary

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

The ENST00000451031.5(ENSG00000223727):​n.339+32846C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 151,896 control chromosomes in the GnomAD database, including 3,848 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 0.22 (3848 hom., cov: 32)
• Consequence: ENSG00000223727 ENST00000451031.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 4 publications found

Genes affected

ENSG00000223727 (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 (SAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451031.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000223727	ENST00000420000.6	TSL:4	n.537+32846C>T		intron	N/A
	ENSG00000223727	ENST00000451031.5	TSL:3	n.339+32846C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33673 AN: 151780 Hom.: 3840 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.222 AC: 33700 AN: 151896 Hom.: 3848 Cov.: 32 AF XY: 0.221 AC XY: 16404 AN XY: 74192

African (AFR) AF: 0.186 AC: 7729 AN: 41472

American (AMR) AF: 0.233 AC: 3547 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1140 AN: 3468

East Asian (EAS) AF: 0.193 AC: 994 AN: 5156

South Asian (SAS) AF: 0.250 AC: 1203 AN: 4804

European-Finnish (FIN) AF: 0.197 AC: 2071 AN: 10538

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16207 AN: 67910

Other (OTH) AF: 0.239 AC: 504 AN: 2106

Alfa AF: 0.223 Hom.: 4302

Bravo AF: 0.223

Asia WGS AF: 0.200 AC: 698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.63
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs10510257; hg19: chr3-3346138;