3-106192692-C-A

Variant names:

• chr3-106192692-C-A
• rs7633167
• ENST00000667697.1:n.185-9822C>A

Variant summary

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

The ENST00000667697.1(ENSG00000287421):​n.185-9822C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 151,844 control chromosomes in the GnomAD database, including 18,450 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 0.46 (18450 hom., cov: 31)
• Consequence: ENSG00000287421 ENST00000667697.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.879
• Publications: 2 publications found

Genes affected

ENSG00000287421 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374027	XR_924311.3	n.212-1108C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287421	ENST00000667697.1	n.185-9822C>A		intron_variant	Intron 2 of 3
ENSG00000287421	ENST00000837046.1	n.195-9822C>A		intron_variant	Intron 2 of 3
ENSG00000308895	ENST00000837134.1	n.233-4168G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70275 AN: 151726 Hom.: 18456 Cov.: 31

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.463 AC: 70278 AN: 151844 Hom.: 18450 Cov.: 31 AF XY: 0.466 AC XY: 34579 AN XY: 74204

African (AFR) AF: 0.195 AC: 8071 AN: 41400

American (AMR) AF: 0.522 AC: 7965 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2133 AN: 3468

East Asian (EAS) AF: 0.579 AC: 2974 AN: 5136

South Asian (SAS) AF: 0.381 AC: 1834 AN: 4808

European-Finnish (FIN) AF: 0.632 AC: 6673 AN: 10554

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.573 AC: 38934 AN: 67916

Other (OTH) AF: 0.506 AC: 1068 AN: 2110

Alfa AF: 0.523 Hom.: 13208

Bravo AF: 0.448

Asia WGS AF: 0.442 AC: 1539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.71
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs7633167; hg19: chr3-105911539;