3-145456001-A-G

Variant names:

• chr3-145456001-A-G
• rs345013
• ENST00000776531.1:n.383-27767T>C

Variant summary

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

The ENST00000776531.1(ENSG00000301137):​n.383-27767T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.099 in 152,186 control chromosomes in the GnomAD database, including 823 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 0.099 (823 hom., cov: 32)
• Consequence: ENSG00000301137 ENST00000776531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 21 publications found

Genes affected

ENSG00000301137 (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 (EAS) allele frequency at 95% confidence interval = 0.141 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
ENSG00000301137	ENST00000776531.1	n.383-27767T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0991 AC: 15069 AN: 152068 Hom.: 825 Cov.: 32

Gnomad AFR AF: 0.0622

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0908

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0822

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.0990 AC: 15062 AN: 152186 Hom.: 823 Cov.: 32 AF XY: 0.0973 AC XY: 7239 AN XY: 74412

African (AFR) AF: 0.0621 AC: 2580 AN: 41544

American (AMR) AF: 0.0908 AC: 1389 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 433 AN: 3472

East Asian (EAS) AF: 0.149 AC: 771 AN: 5158

South Asian (SAS) AF: 0.101 AC: 487 AN: 4824

European-Finnish (FIN) AF: 0.0822 AC: 873 AN: 10616

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8204 AN: 67968

Other (OTH) AF: 0.112 AC: 237 AN: 2108

Alfa AF: 0.114 Hom.: 1952

Bravo AF: 0.0975

Asia WGS AF: 0.136 AC: 471 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.61
DANN	Benign	0.67
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs345013; hg19: chr3-145173788; COSMIC: COSV50192802;