3-3342271-T-G

Variant names:

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

Variant summary

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

The ENST00000420000.6(ENSG00000223727):​n.374-4808A>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 ENST00000420000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150
• Publications: 2 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=-0.79).
• 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

African (AFR) AF: 0.210 AC: 8701 AN: 41470

American (AMR) AF: 0.347 AC: 5301 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3466

East Asian (EAS) AF: 0.410 AC: 2119 AN: 5164

South Asian (SAS) AF: 0.330 AC: 1583 AN: 4804

European-Finnish (FIN) AF: 0.251 AC: 2660 AN: 10582

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17982 AN: 67968

Other (OTH) AF: 0.263 AC: 556 AN: 2116

Alfa AF: 0.265 Hom.: 9397

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
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs10510260; hg19: chr3-3383955;