1-151844596-T-C

Variant names:

• chr1-151844596-T-C
• rs9645406
• ENST00000434182.2:n.353+354T>C

Variant summary

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

The ENST00000434182.2(C2CD4D-AS1):​n.353+354T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 152,100 control chromosomes in the GnomAD database, including 49,601 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 (49601 hom., cov: 31)
• Consequence: C2CD4D-AS1 ENST00000434182.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• Publications: 6 publications found

Genes affected

C2CD4D-AS1 (HGNC:54045): (C2CD4D and THEM5 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434182.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C2CD4D-AS1	NR_024237.2		n.1030+354T>C		intron	N/A
	C2CD4D-AS1	NR_152846.1		n.950+354T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C2CD4D-AS1	ENST00000434182.2	TSL:5	n.353+354T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121914 AN: 151982 Hom.: 49591 Cov.: 31

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.802 AC: 121973 AN: 152100 Hom.: 49601 Cov.: 31 AF XY: 0.806 AC XY: 59914 AN XY: 74364

African (AFR) AF: 0.662 AC: 27407 AN: 41430

American (AMR) AF: 0.785 AC: 11998 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2847 AN: 3470

East Asian (EAS) AF: 0.975 AC: 5041 AN: 5170

South Asian (SAS) AF: 0.811 AC: 3908 AN: 4820

European-Finnish (FIN) AF: 0.895 AC: 9491 AN: 10602

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

European-Non Finnish (NFE) AF: 0.862 AC: 58615 AN: 68000

Other (OTH) AF: 0.798 AC: 1688 AN: 2114

Alfa AF: 0.837 Hom.: 61330

Bravo AF: 0.787

Asia WGS AF: 0.825 AC: 2870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.85
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs9645406; hg19: chr1-151817072;