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. The variant received -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
• Publications: 63 publications found

Genes affected

ENSG00000231681 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000639870.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231681	ENST00000639870.1	TSL:5	n.215-26010C>T		intron	N/A

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

African (AFR) AF: 0.673 AC: 27880 AN: 41418

American (AMR) AF: 0.765 AC: 11678 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2449 AN: 3470

East Asian (EAS) AF: 0.400 AC: 2067 AN: 5164

South Asian (SAS) AF: 0.819 AC: 3947 AN: 4820

European-Finnish (FIN) AF: 0.725 AC: 7671 AN: 10574

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47448 AN: 67956

Other (OTH) AF: 0.678 AC: 1431 AN: 2110

Alfa AF: 0.692 Hom.: 155928

Bravo AF: 0.684

Asia WGS AF: 0.691 AC: 2403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.65
DANN	Benign	0.53
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs1456893; hg19: chr7-50269672;