3-106192692-C-A

Position:

• chr3-106192692-C-A

Variant summary

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

The ENST00000667697.1(ENSG00000287421):​n.185-9822C>A 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 0.463 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: ENST00000667697.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.879

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105374027	XR_924311.3	n.212-1108C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667697.1	n.185-9822C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.506

Alfa AF: 0.523 Hom.: 11965

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7633167; hg19: chr3-105911539;