rs9327919

Variant names:

• chr5-98935021-T-C
• rs9327919
• ENST00000513175.1:n.141+5710T>C

Variant summary

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

The ENST00000513175.1(CHD1-DT):​n.141+5710T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,240 control chromosomes in the GnomAD database, including 1,074 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 0.11 (1074 hom., cov: 32)
• Consequence: CHD1-DT ENST00000513175.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.623
• Publications: 4 publications found

Genes affected

CHD1-DT (HGNC:52907): (CHD1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHD1-DT	NR_151718.1	n.81+6379T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHD1-DT	ENST00000513175.1	n.141+5710T>C		intron_variant	Intron 1 of 2	3
CHD1-DT	ENST00000670964.1	n.124+5710T>C		intron_variant	Intron 1 of 4
CHD1-DT	ENST00000693407.2	n.168+5710T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16355 AN: 152122 Hom.: 1067 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.0972

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.0451

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0735

Gnomad OTH AF: 0.0941

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

GnomAD4 genome AF: 0.108 AC: 16369 AN: 152240 Hom.: 1074 Cov.: 32 AF XY: 0.109 AC XY: 8112 AN XY: 74436

African (AFR) AF: 0.173 AC: 7165 AN: 41520

American (AMR) AF: 0.0971 AC: 1486 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0839 AC: 291 AN: 3468

East Asian (EAS) AF: 0.123 AC: 636 AN: 5186

South Asian (SAS) AF: 0.210 AC: 1013 AN: 4814

European-Finnish (FIN) AF: 0.0451 AC: 478 AN: 10608

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0734 AC: 4996 AN: 68024

Other (OTH) AF: 0.0936 AC: 198 AN: 2116

Alfa AF: 0.0885 Hom.: 1172

Bravo AF: 0.111

Asia WGS AF: 0.155 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	12
DANN	Benign	0.74
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs9327919; hg19: chr5-98270725; COSMIC: COSV63161693;