1-173000982-A-T

Variant names:

• chr1-173000982-A-T
• rs1989627
• ENST00000432694.2:n.224-3300A>T

Variant summary

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

The ENST00000432694.2(ENSG00000224228):​n.224-3300A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.944 in 152,240 control chromosomes in the GnomAD database, including 68,070 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 0.94 (68070 hom., cov: 32)
• Consequence: ENSG00000224228 ENST00000432694.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.930

Genes affected

ENSG00000224228 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.979 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
ENSG00000224228	ENST00000432694.2	n.224-3300A>T		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.944 AC: 143626 AN: 152122 Hom.: 68030 Cov.: 32

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.959

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 0.967

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.952

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

GnomAD4 genome AF: 0.944 AC: 143725 AN: 152240 Hom.: 68070 Cov.: 32 AF XY: 0.944 AC XY: 70263 AN XY: 74448

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.959

Gnomad4 ASJ AF: 0.965

Gnomad4 EAS AF: 0.967

Gnomad4 SAS AF: 0.924

Gnomad4 FIN AF: 0.989

Gnomad4 NFE AF: 0.985

Gnomad4 OTH AF: 0.950

Alfa AF: 0.976 Hom.: 3411

Bravo AF: 0.939

Asia WGS AF: 0.940 AC: 3261 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1989627; hg19: chr1-172970122;