chr3-72460120-T-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377160	XR_940961.3	n.403+995T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305353	ENST00000810549.1	n.412+995T>C		intron_variant	Intron 2 of 2
ENSG00000305353	ENST00000810550.1	n.371+995T>C		intron_variant	Intron 2 of 2
ENSG00000305353	ENST00000810551.1	n.675+995T>C		intron_variant	Intron 2 of 2

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 v4.3

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;