3-106456677-C-T

Variant names:

• chr3-106456677-C-T
• rs722813
• ENST00000668075.2:n.211-6580G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668075.2(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 ENST00000668075.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 3 publications found

Genes affected

ENSG00000291293 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668075.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291293	ENST00000668075.2		n.211-6580G>A		intron	N/A
	ENSG00000291293	ENST00000836909.1		n.98-27739G>A		intron	N/A
	ENSG00000291293	ENST00000836910.1		n.101-27739G>A		intron	N/A

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

African (AFR) AF: 0.736 AC: 30547 AN: 41488

American (AMR) AF: 0.612 AC: 9350 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1538 AN: 3470

East Asian (EAS) AF: 0.567 AC: 2926 AN: 5162

South Asian (SAS) AF: 0.613 AC: 2958 AN: 4824

European-Finnish (FIN) AF: 0.500 AC: 5283 AN: 10556

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.517 AC: 35107 AN: 67948

Other (OTH) AF: 0.596 AC: 1259 AN: 2114

Alfa AF: 0.541 Hom.: 73443

Bravo AF: 0.607

Asia WGS AF: 0.634 AC: 2204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.5
DANN	Benign	0.69
PhyloP100		1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs722813;

hg19: chr3-106175524;