chr1-102212289-T-C

Variant names:

• chr1-102212289-T-C
• rs1938355
• ENST00000447916.1:n.399-12292A>G

Variant summary

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

The ENST00000447916.1(ENSG00000233359):​n.399-12292A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,898 control chromosomes in the GnomAD database, including 8,901 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 0.34 (8901 hom., cov: 32)
• Consequence: ENSG00000233359 ENST00000447916.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.812
• Publications: 0 publications found

Genes affected

ENSG00000233359 (HGNC:58374):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447916.1. 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
	ENSG00000233359	ENST00000447916.1	TSL:3	n.399-12292A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51029 AN: 151778 Hom.: 8885 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.336 AC: 51086 AN: 151898 Hom.: 8901 Cov.: 32 AF XY: 0.336 AC XY: 24963 AN XY: 74228

African (AFR) AF: 0.339 AC: 14028 AN: 41440

American (AMR) AF: 0.385 AC: 5867 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1327 AN: 3466

East Asian (EAS) AF: 0.565 AC: 2914 AN: 5154

South Asian (SAS) AF: 0.338 AC: 1630 AN: 4820

European-Finnish (FIN) AF: 0.244 AC: 2569 AN: 10520

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21570 AN: 67934

Other (OTH) AF: 0.349 AC: 736 AN: 2110

Alfa AF: 0.335 Hom.: 1086

Bravo AF: 0.350

Asia WGS AF: 0.464 AC: 1612 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.9
DANN	Benign	0.78
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs1938355; hg19: chr1-102677845;