chr1-231444306-C-G

Variant names:

• chr1-231444306-C-G
• rs1339896
• ENST00000662216.1:c.30+18132G>C

Variant summary

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

The ENST00000662216.1(ENSG00000287856):​c.30+18132G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,080 control chromosomes in the GnomAD database, including 5,466 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 0.26 (5466 hom., cov: 32)
• Consequence: ENSG00000287856 ENST00000662216.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 2 publications found

Genes affected

ENSG00000287856 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662216.1. 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
	ENSG00000287856	ENST00000662216.1		c.30+18132G>C		intron	N/A	ENSP00000499467.1
	ENSG00000287856	ENST00000653908.1		c.30+18132G>C		intron	N/A	ENSP00000499669.1
	ENSG00000287856	ENST00000653198.1		n.433+18166G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39455 AN: 151962 Hom.: 5456 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0362

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.260 AC: 39494 AN: 152080 Hom.: 5466 Cov.: 32 AF XY: 0.251 AC XY: 18652 AN XY: 74356

African (AFR) AF: 0.297 AC: 12333 AN: 41494

American (AMR) AF: 0.314 AC: 4791 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 799 AN: 3470

East Asian (EAS) AF: 0.0361 AC: 187 AN: 5182

South Asian (SAS) AF: 0.119 AC: 574 AN: 4822

European-Finnish (FIN) AF: 0.183 AC: 1934 AN: 10556

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 18037 AN: 67968

Other (OTH) AF: 0.244 AC: 514 AN: 2108

Alfa AF: 0.258 Hom.: 636

Bravo AF: 0.276

Asia WGS AF: 0.0960 AC: 338 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.5
DANN	Benign	0.66
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1339896; hg19: chr1-231580052;