rs1456893

chr7-50230076-G-Achr7-50230076-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, non coding transcript 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: ENST00000639870.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.890

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000639870.1	n.215-26010C>T		intron_variant, non_coding_transcript_variant		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;