rs4672507

Variant names:

• chr2-62343438-T-A
• rs4672507
• ENST00000687402.3:n.199+46992T>A

Your query was ambiguous. Multiple possible variants found:

• chr2-62343438-T-A
• chr2-62343438-T-C
• chr2-62343438-T-G

Variant summary

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

The ENST00000687402.3(ENSG00000228541):​n.199+46992T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 152,020 control chromosomes in the GnomAD database, including 27,316 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 0.60 (27316 hom., cov: 32)
• Consequence: ENSG00000228541 ENST00000687402.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 13 publications found

Genes affected

ENSG00000228541 (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 = 0.657 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
ENSG00000228541	ENST00000687402.3	n.199+46992T>A		intron_variant	Intron 1 of 1
ENSG00000228541	ENST00000687773.2	n.200-18382T>A		intron_variant	Intron 1 of 1
ENSG00000228541	ENST00000688476.3	n.202-2476T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90839 AN: 151900 Hom.: 27282 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.598 AC: 90938 AN: 152020 Hom.: 27316 Cov.: 32 AF XY: 0.600 AC XY: 44590 AN XY: 74282

African (AFR) AF: 0.539 AC: 22359 AN: 41452

American (AMR) AF: 0.598 AC: 9129 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1915 AN: 3462

East Asian (EAS) AF: 0.596 AC: 3074 AN: 5162

South Asian (SAS) AF: 0.676 AC: 3259 AN: 4822

European-Finnish (FIN) AF: 0.633 AC: 6688 AN: 10566

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42578 AN: 67970

Other (OTH) AF: 0.583 AC: 1231 AN: 2112

Alfa AF: 0.612 Hom.: 3387

Bravo AF: 0.590

Asia WGS AF: 0.633 AC: 2203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.70
PhyloP100		0.0090

Splicing

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

Other links and lift over

dbSNP: rs4672507; hg19: chr2-62570573;