rs1622146

Variant names:

• chr1-231443426-T-C
• rs1622146
• ENST00000662216.1:c.30+19012A>G

Variant summary

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

The ENST00000662216.1(ENSG00000287856):​c.30+19012A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,020 control chromosomes in the GnomAD database, including 9,048 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 0.32 (9048 hom., cov: 32)
• Consequence: ENSG00000287856 ENST00000662216.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287856	ENST00000662216.1	c.30+19012A>G		intron_variant	Intron 3 of 6			ENSP00000499467.1
ENSG00000287856	ENST00000653908.1	c.30+19012A>G		intron_variant	Intron 2 of 4			ENSP00000499669.1
ENSG00000287856	ENST00000653198.1	n.433+19046A>G		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48378 AN: 151902 Hom.: 9021 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0360

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.319 AC: 48453 AN: 152020 Hom.: 9048 Cov.: 32 AF XY: 0.308 AC XY: 22888 AN XY: 74330

African (AFR) AF: 0.502 AC: 20799 AN: 41442

American (AMR) AF: 0.336 AC: 5135 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 799 AN: 3472

East Asian (EAS) AF: 0.0359 AC: 186 AN: 5176

South Asian (SAS) AF: 0.120 AC: 579 AN: 4812

European-Finnish (FIN) AF: 0.184 AC: 1943 AN: 10586

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18070 AN: 67938

Other (OTH) AF: 0.290 AC: 611 AN: 2110

Alfa AF: 0.282 Hom.: 27356

Bravo AF: 0.344

Asia WGS AF: 0.113 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.51
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs1622146; hg19: chr1-231579172;