1-173000982-A-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000432694.2(ENSG00000224000):​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: ENSG00000224000 ENST00000432694.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.930
• Publications: 1 publications found

Genes affected

ENSG00000224000 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000224000	ENST00000432694.2	n.224-3300A>T		intron_variant	Intron 1 of 4	3
ENSG00000224000	ENST00000717048.1	n.324-62891A>T		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.856 AC: 35554 AN: 41530

American (AMR) AF: 0.959 AC: 14676 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.965 AC: 3351 AN: 3472

East Asian (EAS) AF: 0.967 AC: 5017 AN: 5188

South Asian (SAS) AF: 0.924 AC: 4454 AN: 4818

European-Finnish (FIN) AF: 0.989 AC: 10495 AN: 10612

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.985 AC: 67000 AN: 68004

Other (OTH) AF: 0.950 AC: 2007 AN: 2112

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
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs1989627; hg19: chr1-172970122;