ENST00000420000.6:n.537+39500C>T

Variant names:

• chr3-3297800-G-A
• rs10510255
• ENST00000420000.6:n.537+39500C>T

Variant summary

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

The ENST00000420000.6(ENSG00000223727):​n.537+39500C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0254 in 151,902 control chromosomes in the GnomAD database, including 98 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 0.025 (98 hom., cov: 32)
• Consequence: ENSG00000223727 ENST00000420000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.11 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
ENSG00000223727	ENST00000420000.6	n.537+39500C>T		intron_variant	Intron 4 of 4	4
ENSG00000223727	ENST00000451031.5	n.340-31662C>T		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.0254 AC: 3853 AN: 151784 Hom.: 97 Cov.: 32

Gnomad AFR AF: 0.0268

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0235

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.0963

Gnomad FIN AF: 0.00585

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0158

Gnomad OTH AF: 0.0273

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

GnomAD4 genome AF: 0.0254 AC: 3861 AN: 151902 Hom.: 98 Cov.: 32 AF XY: 0.0261 AC XY: 1937 AN XY: 74242

African (AFR) AF: 0.0270 AC: 1118 AN: 41472

American (AMR) AF: 0.0235 AC: 358 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0274 AC: 95 AN: 3464

East Asian (EAS) AF: 0.117 AC: 601 AN: 5124

South Asian (SAS) AF: 0.0968 AC: 466 AN: 4816

European-Finnish (FIN) AF: 0.00585 AC: 62 AN: 10594

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0158 AC: 1072 AN: 67884

Other (OTH) AF: 0.0270 AC: 57 AN: 2108

Alfa AF: 0.0104 Hom.: 5

Bravo AF: 0.0264

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.50
DANN	Benign	0.77
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs10510255; hg19: chr3-3339484;