rs6775191

Variant names:

• chr3-12230699-G-A
• rs6775191
• ENST00000690965.2:n.440+566C>T

Variant summary

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

The ENST00000690965.2(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 ENST00000690965.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212
• Publications: 7 publications found

Genes affected

ENSG00000288952 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000690965.2. 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
	ENSG00000288952	ENST00000690965.2		n.440+566C>T		intron	N/A
	ENSG00000288952	ENST00000764008.1		n.443+566C>T		intron	N/A

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

African (AFR) AF: 0.224 AC: 9275 AN: 41496

American (AMR) AF: 0.242 AC: 3699 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1407 AN: 3470

East Asian (EAS) AF: 0.0341 AC: 177 AN: 5184

South Asian (SAS) AF: 0.157 AC: 755 AN: 4824

European-Finnish (FIN) AF: 0.295 AC: 3118 AN: 10578

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21860 AN: 67990

Other (OTH) AF: 0.296 AC: 624 AN: 2110

Alfa AF: 0.313 Hom.: 13107

Bravo AF: 0.271

Asia WGS AF: 0.125 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.6
DANN	Benign	0.67
PhyloP100		-0.21

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: rs6775191;

hg19: chr3-12272199;