rs4645008

Variant names:

• chr2-226174102-T-C
• rs4645008
• ENST00000719962.1:n.93+11218A>G

Variant summary

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

The ENST00000719962.1(ENSG00000235070):​n.93+11218A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 151,940 control chromosomes in the GnomAD database, including 23,459 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 0.55 (23459 hom., cov: 32)
• Consequence: ENSG00000235070 ENST00000719962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 7 publications found

Genes affected

ENSG00000235070 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC646736	NR_046102.1	n.505-645T>C		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235070	ENST00000719962.1	n.93+11218A>G		intron_variant	Intron 1 of 1
ENSG00000293944	ENST00000720051.1	n.147-645T>C		intron_variant	Intron 1 of 3
ENSG00000293944	ENST00000720052.1	n.123-645T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83087 AN: 151822 Hom.: 23415 Cov.: 32

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.547 AC: 83172 AN: 151940 Hom.: 23459 Cov.: 32 AF XY: 0.552 AC XY: 40969 AN XY: 74264

African (AFR) AF: 0.690 AC: 28574 AN: 41440

American (AMR) AF: 0.532 AC: 8121 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1332 AN: 3470

East Asian (EAS) AF: 0.537 AC: 2763 AN: 5144

South Asian (SAS) AF: 0.455 AC: 2184 AN: 4804

European-Finnish (FIN) AF: 0.591 AC: 6253 AN: 10584

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32268 AN: 67924

Other (OTH) AF: 0.510 AC: 1075 AN: 2106

Alfa AF: 0.520 Hom.: 2637

Bravo AF: 0.553

Asia WGS AF: 0.426 AC: 1480 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.34
DANN	Benign	0.67
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs4645008; hg19: chr2-227038818;