ENST00000665394.1:n.70+14168A>C

Variant names:

• chr1-238253180-A-C
• rs1564505
• ENST00000665394.1:n.70+14168A>C

Variant summary

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

The ENST00000665394.1(ENSG00000234464):​n.70+14168A>C 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 151,534 control chromosomes in the GnomAD database, including 27,561 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 (27561 hom., cov: 31)
• Consequence: ENSG00000234464 ENST00000665394.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

Genes affected

ENSG00000234464 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• 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+14168A>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.600 AC: 90875 AN: 151414 Hom.: 27533 Cov.: 31

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.539

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: 90950 AN: 151534 Hom.: 27561 Cov.: 31 AF XY: 0.608 AC XY: 45002 AN XY: 74036

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.703

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.700

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.592

Alfa AF: 0.600 Hom.: 3570

Bravo AF: 0.606

Asia WGS AF: 0.645 AC: 2237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1564505; hg19: chr1-238416480;