3-197348850-G-A

Variant names:

• chr3-197348850-G-A
• rs768858
• ENST00000794352.1:n.264-2419C>T

Variant summary

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

The ENST00000794352.1(ENSG00000235126):​n.264-2419C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,040 control chromosomes in the GnomAD database, including 2,788 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 0.17 (2788 hom., cov: 32)
• Consequence: ENSG00000235126 ENST00000794352.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590
• Publications: 7 publications found

Genes affected

ENSG00000235126 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794352.1. 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
	ENSG00000235126	ENST00000794352.1		n.264-2419C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26109 AN: 151922 Hom.: 2786 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0543

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.172 AC: 26137 AN: 152040 Hom.: 2788 Cov.: 32 AF XY: 0.174 AC XY: 12931 AN XY: 74340

African (AFR) AF: 0.309 AC: 12791 AN: 41402

American (AMR) AF: 0.142 AC: 2167 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3468

East Asian (EAS) AF: 0.0542 AC: 281 AN: 5180

South Asian (SAS) AF: 0.216 AC: 1040 AN: 4824

European-Finnish (FIN) AF: 0.144 AC: 1524 AN: 10582

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7453 AN: 67994

Other (OTH) AF: 0.152 AC: 320 AN: 2110

Alfa AF: 0.124 Hom.: 3176

Bravo AF: 0.172

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.51
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs768858; hg19: chr3-197075721;