3-12230699-G-A

Position:

• chr3-12230699-G-A

Variant summary

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

The ENST00000690965.1(ENSG00000288952):​n.440+566C>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 0.273 in 152,146 control chromosomes in the GnomAD database, including 6,098 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 0.27 (6098 hom., cov: 32)
• Consequence: ENST00000690965.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000690965.1	n.440+566C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41462 AN: 152028 Hom.: 6089 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.0339

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.273 AC: 41502 AN: 152146 Hom.: 6098 Cov.: 32 AF XY: 0.268 AC XY: 19971 AN XY: 74382

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.0341

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.296

Alfa AF: 0.317 Hom.: 10564

Bravo AF: 0.271

Asia WGS AF: 0.125 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6775191; hg19: chr3-12272199;