1-54168294-G-C

Variant names:

• chr1-54168294-G-C
• rs671431
• ENST00000637610.1:n.304-15113C>G

Variant summary

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

The ENST00000637610.1(ENSG00000256407):​n.304-15113C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 151,918 control chromosomes in the GnomAD database, including 48,604 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 0.80 (48604 hom., cov: 29)
• Consequence: ENSG00000256407 ENST00000637610.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• Publications: 2 publications found

Genes affected

ENSG00000256407 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 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
ENSG00000256407	ENST00000637610.1	n.304-15113C>G		intron_variant	Intron 3 of 9	5		ENSP00000490901.1
ENSG00000256407	ENST00000311841.7	n.*179-15113C>G		intron_variant	Intron 5 of 7	2		ENSP00000457656.1
ENSG00000256407	ENST00000525949.1	n.92+4309C>G		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121141 AN: 151800 Hom.: 48554 Cov.: 29

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.798 AC: 121249 AN: 151918 Hom.: 48604 Cov.: 29 AF XY: 0.799 AC XY: 59331 AN XY: 74256

African (AFR) AF: 0.742 AC: 30769 AN: 41440

American (AMR) AF: 0.844 AC: 12894 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2858 AN: 3472

East Asian (EAS) AF: 0.991 AC: 5084 AN: 5132

South Asian (SAS) AF: 0.743 AC: 3569 AN: 4802

European-Finnish (FIN) AF: 0.824 AC: 8718 AN: 10578

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.807 AC: 54782 AN: 67908

Other (OTH) AF: 0.801 AC: 1691 AN: 2110

Alfa AF: 0.799 Hom.: 5697

Bravo AF: 0.799

Asia WGS AF: 0.852 AC: 2965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.47
PhyloP100		-0.12

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs671431; hg19: chr1-54633967;