3-3399757-T-G

Position:

• chr3-3399757-T-G

Variant summary

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

The ENST00000420000.6(ENSG00000223727):​n.201-17107A>C variant causes a intron, non coding transcript 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: ENST00000420000.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000420000.6	n.201-17107A>C		intron_variant, non_coding_transcript_variant		4
	ENST00000451031.5	n.175+41151A>C		intron_variant, non_coding_transcript_variant		3
	ENST00000455703.1	n.60-17107A>C		intron_variant, non_coding_transcript_variant		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;