rs1667301

Variant names:

• chr2-231559006-A-G
• rs1667301
• ENST00000778820.1:n.644-12917T>C

Variant summary

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

The ENST00000778820.1(ENSG00000286399):​n.644-12917T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 152,058 control chromosomes in the GnomAD database, including 13,084 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 0.41 (13084 hom., cov: 32)
• Consequence: ENSG00000286399 ENST00000778820.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398
• Publications: 10 publications found

Genes affected

ENSG00000286399 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 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
ENSG00000286399	ENST00000778820.1	n.644-12917T>C		intron_variant	Intron 5 of 5
ENSG00000301477	ENST00000779097.1	n.216+4003A>G		intron_variant	Intron 2 of 2
ENSG00000301477	ENST00000779098.1	n.356-2970A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62261 AN: 151940 Hom.: 13081 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.410 AC: 62286 AN: 152058 Hom.: 13084 Cov.: 32 AF XY: 0.405 AC XY: 30098 AN XY: 74314

African (AFR) AF: 0.457 AC: 18934 AN: 41458

American (AMR) AF: 0.364 AC: 5563 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 949 AN: 3468

East Asian (EAS) AF: 0.189 AC: 981 AN: 5178

South Asian (SAS) AF: 0.317 AC: 1528 AN: 4824

European-Finnish (FIN) AF: 0.393 AC: 4151 AN: 10566

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28843 AN: 67982

Other (OTH) AF: 0.378 AC: 799 AN: 2112

Alfa AF: 0.413 Hom.: 26012

Bravo AF: 0.410

Asia WGS AF: 0.209 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.3
DANN	Benign	0.79
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs1667301; hg19: chr2-232423717;