ENST00000432694.2:n.378-3908A>G

Variant names:

• chr1-173012405-A-G
• rs6425196
• ENST00000432694.2:n.378-3908A>G

Variant summary

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

The ENST00000432694.2(ENSG00000224000):​n.378-3908A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.976 in 152,262 control chromosomes in the GnomAD database, including 72,556 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 0.98 (72556 hom., cov: 32)
• Consequence: ENSG00000224000 ENST00000432694.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496
• Publications: 2 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000432694.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000224000	ENST00000432694.2	TSL:3	n.378-3908A>G		intron	N/A
	ENSG00000224000	ENST00000717048.1		n.324-51468A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.976 AC: 148502 AN: 152144 Hom.: 72499 Cov.: 32

Gnomad AFR AF: 0.967

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.971

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.977

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

GnomAD4 genome AF: 0.976 AC: 148617 AN: 152262 Hom.: 72556 Cov.: 32 AF XY: 0.975 AC XY: 72602 AN XY: 74454

African (AFR) AF: 0.967 AC: 40164 AN: 41536

American (AMR) AF: 0.971 AC: 14840 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.965 AC: 3349 AN: 3470

East Asian (EAS) AF: 0.967 AC: 5008 AN: 5180

South Asian (SAS) AF: 0.926 AC: 4462 AN: 4820

European-Finnish (FIN) AF: 0.989 AC: 10505 AN: 10622

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.986 AC: 67059 AN: 68034

Other (OTH) AF: 0.974 AC: 2058 AN: 2112

Alfa AF: 0.978 Hom.: 36616

Bravo AF: 0.975

Asia WGS AF: 0.943 AC: 3280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.70
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs6425196; hg19: chr1-172981545;