3-3399757-T-G

Variant names:

• chr3-3399757-T-G
• rs7645357
• ENST00000420000.6:n.201-17107A>C

Variant summary

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

The ENST00000455703.1(ENSG00000223727):​n.60-17107A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,980 control chromosomes in the GnomAD database, including 16,981 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 0.42 (16981 hom., cov: 32)
• Consequence: ENSG00000223727 ENST00000455703.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 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.201-17107A>C		intron_variant	Intron 2 of 4	4
ENSG00000223727	ENST00000451031.5	n.175+41151A>C		intron_variant	Intron 2 of 5	3
ENSG00000223727	ENST00000455703.1	n.60-17107A>C		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63725 AN: 151862 Hom.: 16951 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.420 AC: 63819 AN: 151980 Hom.: 16981 Cov.: 32 AF XY: 0.419 AC XY: 31117 AN XY: 74270

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.386

Alfa AF: 0.276 Hom.: 6043

Bravo AF: 0.443

Asia WGS AF: 0.583 AC: 2025 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7645357; hg19: chr3-3441441;