chr1-96571527-T-C

Variant names:

• chr1-96571527-T-C
• rs10783050
• ENST00000724711.1:n.183-13850A>G

Variant summary

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

The ENST00000724711.1(ENSG00000294611):​n.183-13850A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,202 control chromosomes in the GnomAD database, including 7,652 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 0.28 (7652 hom., cov: 33)
• Consequence: ENSG00000294611 ENST00000724711.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.86
• Publications: 20 publications found

Genes affected

ENSG00000294611 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.493 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
ENSG00000294611	ENST00000724711.1	n.183-13850A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43111 AN: 152084 Hom.: 7646 Cov.: 33

Gnomad AFR AF: 0.0713

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.283 AC: 43118 AN: 152202 Hom.: 7652 Cov.: 33 AF XY: 0.288 AC XY: 21402 AN XY: 74398

African (AFR) AF: 0.0710 AC: 2952 AN: 41556

American (AMR) AF: 0.340 AC: 5194 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1174 AN: 3472

East Asian (EAS) AF: 0.509 AC: 2637 AN: 5176

South Asian (SAS) AF: 0.370 AC: 1784 AN: 4828

European-Finnish (FIN) AF: 0.410 AC: 4333 AN: 10564

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 23984 AN: 68004

Other (OTH) AF: 0.309 AC: 652 AN: 2108

Alfa AF: 0.327 Hom.: 20660

Bravo AF: 0.272

Asia WGS AF: 0.486 AC: 1686 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	12
DANN	Benign	0.71
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs10783050; hg19: chr1-97037083;