rs618465

Variant names:

• chr1-54162157-A-G
• rs618465
• ENST00000637610.1:n.304-8976T>C

Variant summary

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

The ENST00000637610.1(ENSG00000256407):​n.304-8976T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.855 in 152,236 control chromosomes in the GnomAD database, including 55,688 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 0.85 (55688 hom., cov: 33)
• Consequence: ENSG00000256407 ENST00000637610.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 4 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.884 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.304-8976T>C		intron_variant	Intron 3 of 9	5		ENSP00000490901.1
ENSG00000256407	ENST00000311841.7	n.*179-8976T>C		intron_variant	Intron 5 of 7	2		ENSP00000457656.1
ENSG00000256407	ENST00000525949.1	n.92+10446T>C		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.855 AC: 130006 AN: 152118 Hom.: 55644 Cov.: 33

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.855 AC: 130108 AN: 152236 Hom.: 55688 Cov.: 33 AF XY: 0.852 AC XY: 63383 AN XY: 74420

African (AFR) AF: 0.799 AC: 33194 AN: 41528

American (AMR) AF: 0.887 AC: 13563 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.886 AC: 3075 AN: 3472

East Asian (EAS) AF: 0.763 AC: 3951 AN: 5176

South Asian (SAS) AF: 0.874 AC: 4220 AN: 4828

European-Finnish (FIN) AF: 0.827 AC: 8769 AN: 10606

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.890 AC: 60515 AN: 68014

Other (OTH) AF: 0.858 AC: 1811 AN: 2110

Alfa AF: 0.881 Hom.: 98658

Bravo AF: 0.854

Asia WGS AF: 0.795 AC: 2762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.8
DANN	Benign	0.81
PhyloP100		0.043

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: rs618465; hg19: chr1-54627830;