rs467728

Positions:

• chr5-98953863-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000513175.1(CHD1-DT):​n.142-22908G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,040 control chromosomes in the GnomAD database, including 7,013 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 0.30 (7013 hom., cov: 32)
• Consequence: CHD1-DT ENST00000513175.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

CHD1-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHD1-DT	NR_151718.1	n.81+25221G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHD1-DT	ENST00000513175.1	n.142-22908G>A		intron_variant		3
CHD1-DT	ENST00000670964.1	n.125-12755G>A		intron_variant
CHD1-DT	ENST00000693407.1	n.142-7580G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44829 AN: 151922 Hom.: 7008 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.0958

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.295 AC: 44859 AN: 152040 Hom.: 7013 Cov.: 32 AF XY: 0.284 AC XY: 21143 AN XY: 74338

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.0956

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.282

Alfa AF: 0.305 Hom.: 6794

Bravo AF: 0.305

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.22
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs467728; hg19: chr5-98289567;