rs1614148

Variant names:

• chr1-231462218-C-A
• rs1614148
• ENST00000662216.1:c.30+220G>T

Variant summary

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

The ENST00000662216.1(ENSG00000287856):​c.30+220G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,114 control chromosomes in the GnomAD database, including 4,573 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 0.24 (4573 hom., cov: 32)
• Consequence: ENSG00000287856 ENST00000662216.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180
• Publications: 7 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=-0.67).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.299 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+220G>T		intron_variant	Intron 3 of 6			ENSP00000499467.1
ENSG00000287856	ENST00000653908.1	c.30+220G>T		intron_variant	Intron 2 of 4			ENSP00000499669.1
ENSG00000287856	ENST00000653198.1	n.433+254G>T		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36127 AN: 151996 Hom.: 4568 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0360

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.238 AC: 36144 AN: 152114 Hom.: 4573 Cov.: 32 AF XY: 0.230 AC XY: 17079 AN XY: 74344

African (AFR) AF: 0.222 AC: 9202 AN: 41496

American (AMR) AF: 0.306 AC: 4676 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 797 AN: 3472

East Asian (EAS) AF: 0.0359 AC: 186 AN: 5184

South Asian (SAS) AF: 0.117 AC: 563 AN: 4810

European-Finnish (FIN) AF: 0.183 AC: 1931 AN: 10560

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.264 AC: 17973 AN: 67994

Other (OTH) AF: 0.233 AC: 491 AN: 2110

Alfa AF: 0.265 Hom.: 7053

Bravo AF: 0.252

Asia WGS AF: 0.0880 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	11
DANN	Benign	0.89
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1614148; hg19: chr1-231597964;