1-75969735-A-T

Variant names:

• chr1-75969735-A-T
• rs12405994
• ENST00000635455.1:n.192-13710A>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635455.1(ENSG00000225605):​n.192-13710A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0744 in 152,264 control chromosomes in the GnomAD database, including 638 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 0.074 (638 hom., cov: 32)
• Consequence: ENSG00000225605 ENST00000635455.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

Genes affected

ENSG00000225605 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378806	XR_947521.3	n.225-4649T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225605	ENST00000635455.1	n.192-13710A>T		intron_variant	Intron 2 of 7	5
ENSG00000225605	ENST00000653726.1	n.198-2485A>T		intron_variant	Intron 2 of 7
ENSG00000225605	ENST00000654326.1	n.246-2485A>T		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.0743 AC: 11300 AN: 152146 Hom.: 633 Cov.: 32

Gnomad AFR AF: 0.0349

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.0639

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0704

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0744 AC: 11332 AN: 152264 Hom.: 638 Cov.: 32 AF XY: 0.0778 AC XY: 5794 AN XY: 74454

Gnomad4 AFR AF: 0.0352

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.0527

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.0648

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0704

Gnomad4 OTH AF: 0.0734

Alfa AF: 0.0380 Hom.: 41

Bravo AF: 0.0787

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.0
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12405994; hg19: chr1-76435420;