3-3417876-C-G

Position:

• chr3-3417876-C-G

Variant summary

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

The ENST00000420000.6(ENSG00000223727):​n.201-35226G>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 0.638 in 151,770 control chromosomes in the GnomAD database, including 31,300 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 0.64 (31300 hom., cov: 31)
• Consequence: ENST00000420000.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.669 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.201-35226G>C		intron_variant, non_coding_transcript_variant		4
	ENST00000451031.5	n.175+23032G>C		intron_variant, non_coding_transcript_variant		3
	ENST00000455703.1	n.60-35226G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96716 AN: 151648 Hom.: 31273 Cov.: 31

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.638 AC: 96790 AN: 151770 Hom.: 31300 Cov.: 31 AF XY: 0.641 AC XY: 47524 AN XY: 74172

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.647

Alfa AF: 0.502 Hom.: 1158

Bravo AF: 0.628

Asia WGS AF: 0.583 AC: 2020 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.091
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4685635; hg19: chr3-3459560;