rs4567344

Variant names:

• chr1-235107459-C-T
• rs4567344
• ENST00000812313.1:n.268-1604C>T

Variant summary

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

The ENST00000812313.1(ENSG00000305676):​n.268-1604C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 152,164 control chromosomes in the GnomAD database, including 49,134 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 0.79 (49134 hom., cov: 32)
• Consequence: ENSG00000305676 ENST00000812313.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 6 publications found

Genes affected

ENSG00000305676 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812313.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305676	ENST00000812313.1		n.268-1604C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120785 AN: 152046 Hom.: 49086 Cov.: 32

Gnomad AFR AF: 0.951

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.794 AC: 120884 AN: 152164 Hom.: 49134 Cov.: 32 AF XY: 0.793 AC XY: 58948 AN XY: 74382

African (AFR) AF: 0.951 AC: 39506 AN: 41536

American (AMR) AF: 0.702 AC: 10724 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2557 AN: 3472

East Asian (EAS) AF: 0.419 AC: 2172 AN: 5178

South Asian (SAS) AF: 0.754 AC: 3632 AN: 4818

European-Finnish (FIN) AF: 0.797 AC: 8435 AN: 10582

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51400 AN: 67986

Other (OTH) AF: 0.748 AC: 1576 AN: 2108

Alfa AF: 0.755 Hom.: 81993

Bravo AF: 0.789

Asia WGS AF: 0.605 AC: 2105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.56
DANN	Benign	0.35
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4567344;

hg19: chr1-235270774;