rs467728

Variant names:

• chr5-98953863-G-A
• rs467728
• ENST00000513175.1:n.142-22908G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513175.1. 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
	CHD1-DT	NR_151718.1		n.81+25221G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHD1-DT	ENST00000513175.1	TSL:3	n.142-22908G>A		intron	N/A
	CHD1-DT	ENST00000670964.1		n.125-12755G>A		intron	N/A
	CHD1-DT	ENST00000693407.2		n.169-7580G>A		intron	N/A

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

African (AFR) AF: 0.366 AC: 15166 AN: 41410

American (AMR) AF: 0.228 AC: 3486 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1252 AN: 3470

East Asian (EAS) AF: 0.0956 AC: 496 AN: 5186

South Asian (SAS) AF: 0.217 AC: 1047 AN: 4828

European-Finnish (FIN) AF: 0.155 AC: 1637 AN: 10566

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20777 AN: 67976

Other (OTH) AF: 0.282 AC: 597 AN: 2116

Alfa AF: 0.306 Hom.: 9082

Bravo AF: 0.305

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.22
DANN	Benign	0.73
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: rs467728;

hg19: chr5-98289567;