chr3-193772960-A-G

Variant names:

• chr3-193772960-A-G
• rs6770515
• ENST00000664530.1:n.565+522A>G

Variant summary

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

The ENST00000664530.1(ENSG00000287206):​n.565+522A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 152,048 control chromosomes in the GnomAD database, including 23,748 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 0.55 (23748 hom., cov: 32)
• Consequence: ENSG00000287206 ENST00000664530.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 4 publications found

Genes affected

ENSG00000287206 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664530.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287206	ENST00000664530.1		n.565+522A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83726 AN: 151930 Hom.: 23729 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.551 AC: 83796 AN: 152048 Hom.: 23748 Cov.: 32 AF XY: 0.557 AC XY: 41371 AN XY: 74324

African (AFR) AF: 0.414 AC: 17141 AN: 41434

American (AMR) AF: 0.591 AC: 9042 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1764 AN: 3470

East Asian (EAS) AF: 0.489 AC: 2522 AN: 5158

South Asian (SAS) AF: 0.595 AC: 2866 AN: 4814

European-Finnish (FIN) AF: 0.696 AC: 7361 AN: 10574

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41243 AN: 67992

Other (OTH) AF: 0.546 AC: 1153 AN: 2112

Alfa AF: 0.577 Hom.: 5378

Bravo AF: 0.534

Asia WGS AF: 0.554 AC: 1928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.1
DANN	Benign	0.30
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs6770515; hg19: chr3-193490749;