1-238253983-A-G

Variant names:

• chr1-238253983-A-G
• rs6682403
• ENST00000665394.1:n.70+14971A>G

Variant summary

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

The ENST00000665394.1(ENSG00000234464):​n.70+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 ENST00000665394.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561

Genes affected

ENSG00000234464 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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	ENST00000665394.1	n.70+14971A>G		intron_variant	Intron 1 of 4

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

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.702

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.593

Alfa AF: 0.587 Hom.: 12984

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6682403; hg19: chr1-238417283;