rs10914967

Variant names:

• chr1-34523636-G-A
• rs10914967
• ENST00000824030.1:n.136+35478C>T

Variant summary

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

The ENST00000824030.1(ENSG00000307130):​n.136+35478C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,120 control chromosomes in the GnomAD database, including 10,221 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 0.35 (10221 hom., cov: 33)
• Consequence: ENSG00000307130 ENST00000824030.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.389
• Publications: 7 publications found

Genes affected

ENSG00000307130 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378641	XR_001737964.2	n.577+23943C>T		intron_variant	Intron 5 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307130	ENST00000824030.1	n.136+35478C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52667 AN: 152002 Hom.: 10209 Cov.: 33

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.347 AC: 52718 AN: 152120 Hom.: 10221 Cov.: 33 AF XY: 0.351 AC XY: 26063 AN XY: 74354

African (AFR) AF: 0.512 AC: 21247 AN: 41466

American (AMR) AF: 0.367 AC: 5606 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1044 AN: 3472

East Asian (EAS) AF: 0.367 AC: 1888 AN: 5148

South Asian (SAS) AF: 0.483 AC: 2332 AN: 4824

European-Finnish (FIN) AF: 0.248 AC: 2627 AN: 10594

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17055 AN: 68004

Other (OTH) AF: 0.321 AC: 678 AN: 2114

Alfa AF: 0.282 Hom.: 16372

Bravo AF: 0.360

Asia WGS AF: 0.460 AC: 1600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	14
DANN	Benign	0.89
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs10914967; hg19: chr1-34989237;