3-106456677-C-T

Variant names:

• chr3-106456677-C-T
• rs722813
• ENST00000668075.1:n.211-6580G>A

Variant summary

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

The ENST00000668075.1(ENSG00000291293):​n.211-6580G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 152,040 control chromosomes in the GnomAD database, including 27,240 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 0.59 (27240 hom., cov: 32)
• Consequence: ENSG00000291293 ENST00000668075.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

Genes affected

ENSG00000291293 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929485	XR_007095992.1	n.1050-27739G>A		intron_variant	Intron 5 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291293	ENST00000668075.1	n.211-6580G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89597 AN: 151920 Hom.: 27176 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.590 AC: 89724 AN: 152040 Hom.: 27240 Cov.: 32 AF XY: 0.588 AC XY: 43705 AN XY: 74320

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.596

Alfa AF: 0.525 Hom.: 27658

Bravo AF: 0.607

Asia WGS AF: 0.634 AC: 2204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.5
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs722813; hg19: chr3-106175524;