rs4664679

Variant names:

• chr2-150611962-G-A
• rs4664679
• ENST00000421624.1:n.79+8027C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-150611962-G-A
• chr2-150611962-G-C

Variant summary

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

The ENST00000421624.1(ENSG00000232359):​n.79+8027C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,868 control chromosomes in the GnomAD database, including 14,559 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 0.43 (14559 hom., cov: 31)
• Consequence: ENSG00000232359 ENST00000421624.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 3 publications found

Genes affected

ENSG00000232359 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.57 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
ENSG00000232359	ENST00000421624.1	n.79+8027C>T		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64607 AN: 151746 Hom.: 14553 Cov.: 31

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.426 AC: 64629 AN: 151868 Hom.: 14559 Cov.: 31 AF XY: 0.428 AC XY: 31727 AN XY: 74214

African (AFR) AF: 0.274 AC: 11369 AN: 41438

American (AMR) AF: 0.451 AC: 6880 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2022 AN: 3470

East Asian (EAS) AF: 0.451 AC: 2319 AN: 5140

South Asian (SAS) AF: 0.588 AC: 2828 AN: 4812

European-Finnish (FIN) AF: 0.436 AC: 4591 AN: 10528

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.486 AC: 33002 AN: 67924

Other (OTH) AF: 0.486 AC: 1026 AN: 2112

Alfa AF: 0.436 Hom.: 2451

Bravo AF: 0.415

Asia WGS AF: 0.549 AC: 1903 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.32
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs4664679; hg19: chr2-151468476;