3-194078012-A-T

Position:

• chr3-194078012-A-T

Variant summary

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

The ENST00000655827.1(ENSG00000276407):​n.61-200A>T 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 0.768 in 152,138 control chromosomes in the GnomAD database, including 45,264 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 0.77 (45264 hom., cov: 32)
• Consequence: ENST00000655827.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.898

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724877	XR_007096295.1	n.132-200A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000655827.1	n.61-200A>T		intron_variant, non_coding_transcript_variant
	ENST00000615240.1	n.89-200A>T		intron_variant, non_coding_transcript_variant		5
	ENST00000615650.4	n.28-200A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116738 AN: 152020 Hom.: 45212 Cov.: 32

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.768 AC: 116849 AN: 152138 Hom.: 45264 Cov.: 32 AF XY: 0.774 AC XY: 57542 AN XY: 74372

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.742

Alfa AF: 0.743 Hom.: 5246

Bravo AF: 0.772

Asia WGS AF: 0.869 AC: 3018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.2
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1463697; hg19: chr3-193795801;