1-238253983-A-G

Variant names:

• chr1-238253983-A-G
• rs6682403
• ENST00000422844.2:n.74+14971A>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+14971A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 151,948 control chromosomes in the GnomAD database, including 27,765 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 (27765 hom., cov: 31)
• Consequence: ENSG00000234464 ENST00000422844.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561
• Publications: 2 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.692 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+14971A>G		intron_variant	Intron 1 of 3	3
ENSG00000234464	ENST00000665394.1	n.70+14971A>G		intron_variant	Intron 1 of 4
ENSG00000234464	ENST00000716147.1	n.245+2435A>G		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91301 AN: 151828 Hom.: 27737 Cov.: 31

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.601 AC: 91376 AN: 151948 Hom.: 27765 Cov.: 31 AF XY: 0.609 AC XY: 45237 AN XY: 74274

African (AFR) AF: 0.554 AC: 22964 AN: 41422

American (AMR) AF: 0.703 AC: 10734 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2250 AN: 3472

East Asian (EAS) AF: 0.702 AC: 3618 AN: 5154

South Asian (SAS) AF: 0.588 AC: 2828 AN: 4806

European-Finnish (FIN) AF: 0.683 AC: 7214 AN: 10564

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

European-Non Finnish (NFE) AF: 0.586 AC: 39831 AN: 67952

Other (OTH) AF: 0.593 AC: 1253 AN: 2112

Alfa AF: 0.592 Hom.: 18939

Bravo AF: 0.606

Asia WGS AF: 0.645 AC: 2238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.65
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs6682403; hg19: chr1-238417283;