1-29604254-T-C

Variant names:

• chr1-29604254-T-C
• rs9286938
• ENST00000772656.1:n.173+19592T>C

Variant summary

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

The ENST00000772656.1(ENSG00000300547):​n.173+19592T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.826 in 151,740 control chromosomes in the GnomAD database, including 51,862 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 0.83 (51862 hom., cov: 29)
• Consequence: ENSG00000300547 ENST00000772656.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586
• Publications: 4 publications found

Genes affected

ENSG00000300547 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.851 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
ENSG00000300547	ENST00000772656.1	n.173+19592T>C		intron_variant	Intron 2 of 4
ENSG00000300547	ENST00000772657.1	n.187+19592T>C		intron_variant	Intron 2 of 3
ENSG00000300547	ENST00000772658.1	n.170+19592T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125222 AN: 151622 Hom.: 51826 Cov.: 29

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.826 AC: 125313 AN: 151740 Hom.: 51862 Cov.: 29 AF XY: 0.826 AC XY: 61193 AN XY: 74116

African (AFR) AF: 0.826 AC: 34135 AN: 41338

American (AMR) AF: 0.822 AC: 12542 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.828 AC: 2871 AN: 3468

East Asian (EAS) AF: 0.632 AC: 3242 AN: 5132

South Asian (SAS) AF: 0.873 AC: 4182 AN: 4790

European-Finnish (FIN) AF: 0.822 AC: 8626 AN: 10488

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.837 AC: 56897 AN: 67948

Other (OTH) AF: 0.819 AC: 1729 AN: 2110

Alfa AF: 0.837 Hom.: 26829

Bravo AF: 0.823

Asia WGS AF: 0.766 AC: 2667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.77
DANN	Benign	0.46
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs9286938; hg19: chr1-30077101; COSMIC: COSV59933727;