ENST00000810549.1:n.412+995T>C

Variant names:

• chr3-72460120-T-C
• rs11128271
• ENST00000810549.1:n.412+995T>C

Variant summary

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

The ENST00000810549.1(ENSG00000305353):​n.412+995T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.884 in 152,098 control chromosomes in the GnomAD database, including 59,847 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 0.88 (59847 hom., cov: 33)
• Consequence: ENSG00000305353 ENST00000810549.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565
• Publications: 3 publications found

Genes affected

ENSG00000305353 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810549.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305353	ENST00000810549.1		n.412+995T>C		intron	N/A
	ENSG00000305353	ENST00000810550.1		n.371+995T>C		intron	N/A
	ENSG00000305353	ENST00000810551.1		n.675+995T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134396 AN: 151978 Hom.: 59814 Cov.: 33

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.970

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.884 AC: 134483 AN: 152098 Hom.: 59847 Cov.: 33 AF XY: 0.881 AC XY: 65473 AN XY: 74322

African (AFR) AF: 0.788 AC: 32708 AN: 41492

American (AMR) AF: 0.888 AC: 13576 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.970 AC: 3369 AN: 3472

East Asian (EAS) AF: 0.821 AC: 4238 AN: 5164

South Asian (SAS) AF: 0.838 AC: 4044 AN: 4824

European-Finnish (FIN) AF: 0.877 AC: 9250 AN: 10542

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.945 AC: 64249 AN: 67998

Other (OTH) AF: 0.897 AC: 1895 AN: 2112

Alfa AF: 0.880 Hom.: 26648

Bravo AF: 0.881

Asia WGS AF: 0.803 AC: 2793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	5.9
DANN	Benign	0.89
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs11128271; hg19: chr3-72509271;