3-182722347-C-T

Variant names:

• chr3-182722347-C-T
• rs2700868
• ENST00000788512.1:n.206+18642C>T

Variant summary

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

The ENST00000788512.1(ENSG00000302649):​n.206+18642C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,138 control chromosomes in the GnomAD database, including 3,256 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 0.20 (3256 hom., cov: 31)
• Consequence: ENSG00000302649 ENST00000788512.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 1 publications found

Genes affected

ENSG00000302649 (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 (EAS) allele frequency at 95% confidence interval = 0.307 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
ENSG00000302649	ENST00000788512.1	n.206+18642C>T		intron_variant	Intron 1 of 3
ENSG00000302649	ENST00000788513.1	n.201+18642C>T		intron_variant	Intron 1 of 3
ENSG00000302649	ENST00000788514.1	n.201+18642C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30168 AN: 152020 Hom.: 3245 Cov.: 31

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.199 AC: 30204 AN: 152138 Hom.: 3256 Cov.: 31 AF XY: 0.200 AC XY: 14881 AN XY: 74360

African (AFR) AF: 0.205 AC: 8512 AN: 41502

American (AMR) AF: 0.265 AC: 4047 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1118 AN: 3468

East Asian (EAS) AF: 0.320 AC: 1654 AN: 5164

South Asian (SAS) AF: 0.160 AC: 771 AN: 4810

European-Finnish (FIN) AF: 0.161 AC: 1711 AN: 10604

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11742 AN: 67998

Other (OTH) AF: 0.204 AC: 429 AN: 2102

Alfa AF: 0.183 Hom.: 6571

Bravo AF: 0.207

Asia WGS AF: 0.260 AC: 901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.44
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs2700868; hg19: chr3-182440135;