3-3342271-T-G

Variant names:

• chr3-3342271-T-G
• rs10510260
• ENST00000420000.6:n.374-4808A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000455703.1(ENSG00000223727):​n.233-4808A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,050 control chromosomes in the GnomAD database, including 5,488 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 0.26 (5488 hom., cov: 32)
• Consequence: ENSG00000223727 ENST00000455703.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 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.374-4808A>C		intron_variant	Intron 3 of 4	4
ENSG00000223727	ENST00000451031.5	n.176-4808A>C		intron_variant	Intron 2 of 5	3
ENSG00000223727	ENST00000455703.1	n.233-4808A>C		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40163 AN: 151932 Hom.: 5486 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.264 AC: 40180 AN: 152050 Hom.: 5488 Cov.: 32 AF XY: 0.268 AC XY: 19932 AN XY: 74326

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.263

Alfa AF: 0.263 Hom.: 7410

Bravo AF: 0.268

Asia WGS AF: 0.363 AC: 1257 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510260; hg19: chr3-3383955;