1-238253244-A-G

Variant names:

• chr1-238253244-A-G
• rs4382714
• ENST00000422844.2:n.74+14232A>G

Variant summary

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

The ENST00000422844.2(ENSG00000234464):​n.74+14232A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 151,550 control chromosomes in the GnomAD database, including 27,570 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 0.60 (27570 hom., cov: 32)
• Consequence: ENSG00000234464 ENST00000422844.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 1 publications found

Genes affected

ENSG00000234464 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.691 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
ENSG00000234464	ENST00000422844.2	n.74+14232A>G		intron_variant	Intron 1 of 3	3
ENSG00000234464	ENST00000665394.1	n.70+14232A>G		intron_variant	Intron 1 of 4
ENSG00000234464	ENST00000716147.1	n.245+1696A>G		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.600 AC: 90890 AN: 151434 Hom.: 27543 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.600 AC: 90963 AN: 151550 Hom.: 27570 Cov.: 32 AF XY: 0.608 AC XY: 45006 AN XY: 74044

African (AFR) AF: 0.553 AC: 22871 AN: 41342

American (AMR) AF: 0.702 AC: 10680 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2244 AN: 3464

East Asian (EAS) AF: 0.702 AC: 3607 AN: 5140

South Asian (SAS) AF: 0.587 AC: 2826 AN: 4814

European-Finnish (FIN) AF: 0.681 AC: 7149 AN: 10500

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39656 AN: 67774

Other (OTH) AF: 0.593 AC: 1250 AN: 2108

Alfa AF: 0.611 Hom.: 4779

Bravo AF: 0.606

Asia WGS AF: 0.645 AC: 2239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.61
PhyloP100		0.010

Splicing

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

Other links and lift over

dbSNP: rs4382714; hg19: chr1-238416544;