rs6775191

Variant names:

• chr3-12230699-G-A
• rs6775191
• ENST00000690965.1:n.440+566C>T

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 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: ENSG00000288952 ENST00000690965.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212

Genes affected

ENSG00000288952 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288952	ENST00000690965.1	n.440+566C>T		intron_variant	Intron 2 of 3

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;