3-191738510-C-T

Variant names:

• chr3-191738510-C-T
• rs709087
• ENST00000819945.1:n.349-21004C>T

Variant summary

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

The ENST00000819945.1(ENSG00000306648):​n.349-21004C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,058 control chromosomes in the GnomAD database, including 4,286 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 0.22 (4286 hom., cov: 32)
• Consequence: ENSG00000306648 ENST00000819945.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 3 publications found

Genes affected

ENSG00000306648 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 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
ENSG00000306648	ENST00000819945.1	n.349-21004C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33760 AN: 151942 Hom.: 4279 Cov.: 32

Gnomad AFR AF: 0.0866

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.222 AC: 33777 AN: 152058 Hom.: 4286 Cov.: 32 AF XY: 0.228 AC XY: 16942 AN XY: 74328

African (AFR) AF: 0.0864 AC: 3584 AN: 41500

American (AMR) AF: 0.229 AC: 3495 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 878 AN: 3468

East Asian (EAS) AF: 0.316 AC: 1627 AN: 5148

South Asian (SAS) AF: 0.305 AC: 1474 AN: 4826

European-Finnish (FIN) AF: 0.312 AC: 3295 AN: 10568

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.272 AC: 18492 AN: 67976

Other (OTH) AF: 0.223 AC: 472 AN: 2116

Alfa AF: 0.243 Hom.: 2547

Bravo AF: 0.212

Asia WGS AF: 0.323 AC: 1123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.4
DANN	Benign	0.72
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs709087; hg19: chr3-191456299;