3-118443776-T-C

Variant names:

• chr3-118443776-T-C
• rs10511378
• ENST00000482142.5:n.232+52847A>G

Variant summary

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

The ENST00000833975.1(ENSG00000243276):​n.448+52847A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,218 control chromosomes in the GnomAD database, including 2,062 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 0.16 (2062 hom., cov: 33)
• Consequence: ENSG00000243276 ENST00000833975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 7 publications found

Genes affected

ENSG00000243276 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000833975.1. 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
	ENSG00000243276	ENST00000482142.5	TSL:5	n.232+52847A>G		intron	N/A
	ENSG00000243276	ENST00000833975.1		n.448+52847A>G		intron	N/A
	ENSG00000243276	ENST00000833976.1		n.349+52847A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24015 AN: 152100 Hom.: 2059 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0217

Gnomad SAS AF: 0.0935

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.158 AC: 24035 AN: 152218 Hom.: 2062 Cov.: 33 AF XY: 0.154 AC XY: 11475 AN XY: 74442

African (AFR) AF: 0.206 AC: 8561 AN: 41514

American (AMR) AF: 0.111 AC: 1702 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 785 AN: 3472

East Asian (EAS) AF: 0.0216 AC: 112 AN: 5184

South Asian (SAS) AF: 0.0938 AC: 452 AN: 4818

European-Finnish (FIN) AF: 0.136 AC: 1444 AN: 10620

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.153 AC: 10391 AN: 68000

Other (OTH) AF: 0.155 AC: 327 AN: 2112

Alfa AF: 0.154 Hom.: 6377

Bravo AF: 0.159

Asia WGS AF: 0.0900 AC: 315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.73
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs10511378; hg19: chr3-118162623;