rs2218778

Positions:

• chr3-3462068-A-G
• chr3-3462068-A-T

Variant summary

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

The ENST00000420000.6(ENSG00000223727):​n.201-79418T>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 0.403 in 152,082 control chromosomes in the GnomAD database, including 14,819 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 0.40 (14819 hom., cov: 33)
• Consequence: ENST00000420000.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.422

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.801 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.201-79418T>C		intron_variant, non_coding_transcript_variant		4
	ENST00000451031.5	n.78-21063T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000455703.1	n.59+21971T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61244 AN: 151964 Hom.: 14805 Cov.: 33

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.403 AC: 61316 AN: 152082 Hom.: 14819 Cov.: 33 AF XY: 0.404 AC XY: 30041 AN XY: 74320

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.368

Alfa AF: 0.297 Hom.: 9249

Bravo AF: 0.419

Asia WGS AF: 0.575 AC: 1996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2218778; hg19: chr3-3503752;