rs1895943

Variant names:

• chr12-107847055-C-A
• rs1895943
• ENST00000547452.5:n.327-951G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-107847055-C-A
• chr12-107847055-C-T

Variant summary

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

The ENST00000547452.5(ENSG00000257398):​n.327-951G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 152,222 control chromosomes in the GnomAD database, including 59,025 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 0.88 (59025 hom., cov: 33)
• Consequence: ENSG00000257398 ENST00000547452.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480

Genes affected

ENSG00000257398 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.943 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
ENSG00000257398	ENST00000547452.5	n.327-951G>T		intron_variant	Intron 2 of 4	5
ENSG00000257398	ENST00000551629.2	n.122-938G>T		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.876 AC: 133177 AN: 152104 Hom.: 58988 Cov.: 33

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.931

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.875 AC: 133265 AN: 152222 Hom.: 59025 Cov.: 33 AF XY: 0.870 AC XY: 64779 AN XY: 74438

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.931

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.932

Gnomad4 NFE AF: 0.949

Gnomad4 OTH AF: 0.875

Alfa AF: 0.923 Hom.: 79618

Bravo AF: 0.869

Asia WGS AF: 0.627 AC: 2184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1895943; hg19: chr12-108240832;