rs1893008

Variant names:

• chr11-72183542-G-A
• rs1893008
• ENST00000378140.3:n.419+14971C>T

Variant summary

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

The ENST00000378140.3(ENSG00000204971):​n.419+14971C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.017 in 152,226 control chromosomes in the GnomAD database, including 42 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 0.017 (42 hom., cov: 32)
• Consequence: ENSG00000204971 ENST00000378140.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.76

Genes affected

ENSG00000204971 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0694 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
ENSG00000204971	ENST00000378140.3	n.419+14971C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0169 AC: 2572 AN: 152108 Hom.: 40 Cov.: 32

Gnomad AFR AF: 0.0179

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0138

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.0756

Gnomad SAS AF: 0.0644

Gnomad FIN AF: 0.0135

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00942

Gnomad OTH AF: 0.0172

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

GnomAD4 genome AF: 0.0170 AC: 2585 AN: 152226 Hom.: 42 Cov.: 32 AF XY: 0.0186 AC XY: 1381 AN XY: 74436

Gnomad4 AFR AF: 0.0182

Gnomad4 AMR AF: 0.0138

Gnomad4 ASJ AF: 0.0248

Gnomad4 EAS AF: 0.0756

Gnomad4 SAS AF: 0.0643

Gnomad4 FIN AF: 0.0135

Gnomad4 NFE AF: 0.00944

Gnomad4 OTH AF: 0.0166

Alfa AF: 0.0136 Hom.: 2

Bravo AF: 0.0166

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.14
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1893008; hg19: chr11-71894586;