rs1456893

Variant names:

• chr7-50230076-G-A
• rs1456893
• ENST00000639870.1:n.215-26010C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-50230076-G-A
• chr7-50230076-G-C

Variant summary

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

The ENST00000639870.1(ENSG00000231681):​n.215-26010C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 151,984 control chromosomes in the GnomAD database, including 36,879 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 0.69 (36879 hom., cov: 31)
• Consequence: ENSG00000231681 ENST00000639870.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.890

Genes affected

ENSG00000231681 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.798 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
ENSG00000231681	ENST00000639870.1	n.215-26010C>T		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105220 AN: 151866 Hom.: 36842 Cov.: 31

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.693 AC: 105307 AN: 151984 Hom.: 36879 Cov.: 31 AF XY: 0.696 AC XY: 51730 AN XY: 74284

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.678

Alfa AF: 0.693 Hom.: 81177

Bravo AF: 0.684

Asia WGS AF: 0.691 AC: 2403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.65
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1456893; hg19: chr7-50269672;