rs10925567

Variant names:

• chr1-238121211-T-A
• rs10925567
• ENST00000780747.1:n.360+4547T>A

Variant summary

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

The ENST00000780747.1(ENSG00000301680):​n.360+4547T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0526 in 152,272 control chromosomes in the GnomAD database, including 260 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 0.053 (260 hom., cov: 32)
• Consequence: ENSG00000301680 ENST00000780747.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449
• Publications: 1 publications found

Genes affected

ENSG00000301680 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.089 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
ENSG00000301680	ENST00000780747.1	n.360+4547T>A		intron_variant	Intron 1 of 1
ENSG00000301680	ENST00000780748.1	n.340+4547T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0525 AC: 7992 AN: 152154 Hom.: 259 Cov.: 32

Gnomad AFR AF: 0.0912

Gnomad AMI AF: 0.0176

Gnomad AMR AF: 0.0259

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.0209

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0460

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0526 AC: 8008 AN: 152272 Hom.: 260 Cov.: 32 AF XY: 0.0506 AC XY: 3772 AN XY: 74478

African (AFR) AF: 0.0914 AC: 3796 AN: 41538

American (AMR) AF: 0.0259 AC: 396 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0331 AC: 115 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5178

South Asian (SAS) AF: 0.0499 AC: 241 AN: 4830

European-Finnish (FIN) AF: 0.0209 AC: 222 AN: 10620

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0460 AC: 3127 AN: 68020

Other (OTH) AF: 0.0402 AC: 85 AN: 2116

Alfa AF: 0.0521 Hom.: 25

Bravo AF: 0.0528

Asia WGS AF: 0.0370 AC: 127 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.085
DANN	Benign	0.30
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs10925567; hg19: chr1-238284511;