chr1-188116702-T-C

Variant names:

• chr1-188116702-T-C
• rs10489764
• ENST00000648838.2:n.534+19484T>C

Variant summary

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

The ENST00000648838.2(ENSG00000285894):​n.534+19484T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,952 control chromosomes in the GnomAD database, including 5,345 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 0.25 (5345 hom., cov: 32)
• Consequence: ENSG00000285894 ENST00000648838.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620
• Publications: 5 publications found

Genes affected

ENSG00000285894 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648838.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285894	ENST00000648838.2		n.534+19484T>C		intron	N/A
	ENSG00000285894	ENST00000733149.1		n.243+19484T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38595 AN: 151834 Hom.: 5336 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.254 AC: 38632 AN: 151952 Hom.: 5345 Cov.: 32 AF XY: 0.255 AC XY: 18964 AN XY: 74274

African (AFR) AF: 0.157 AC: 6495 AN: 41490

American (AMR) AF: 0.277 AC: 4230 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1097 AN: 3464

East Asian (EAS) AF: 0.198 AC: 1024 AN: 5162

South Asian (SAS) AF: 0.175 AC: 843 AN: 4824

European-Finnish (FIN) AF: 0.312 AC: 3300 AN: 10564

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.306 AC: 20752 AN: 67872

Other (OTH) AF: 0.253 AC: 534 AN: 2110

Alfa AF: 0.292 Hom.: 28583

Bravo AF: 0.252

Asia WGS AF: 0.195 AC: 676 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.92
DANN	Benign	0.46
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs10489764; hg19: chr1-188085833;