rs4672448

Variant names:

• chr2-61700965-A-C
• rs4672448
• ENST00000753764.1:n.265-17908T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-61700965-A-C
• chr2-61700965-A-G
• chr2-61700965-A-T

Variant summary

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

The ENST00000753764.1(ENSG00000289410):​n.265-17908T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.863 in 152,202 control chromosomes in the GnomAD database, including 56,714 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 0.86 (56714 hom., cov: 32)
• Consequence: ENSG00000289410 ENST00000753764.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 5 publications found

Genes affected

ENSG00000289410 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 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
ENSG00000289410	ENST00000753764.1	n.265-17908T>G		intron_variant	Intron 2 of 3
ENSG00000289410	ENST00000753765.1	n.348-17908T>G		intron_variant	Intron 2 of 2
ENSG00000289410	ENST00000753766.1	n.240-11194T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.862 AC: 131152 AN: 152084 Hom.: 56645 Cov.: 32

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.847

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.856

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

GnomAD4 genome AF: 0.863 AC: 131282 AN: 152202 Hom.: 56714 Cov.: 32 AF XY: 0.866 AC XY: 64465 AN XY: 74418

African (AFR) AF: 0.826 AC: 34294 AN: 41516

American (AMR) AF: 0.902 AC: 13792 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2860 AN: 3468

East Asian (EAS) AF: 0.934 AC: 4837 AN: 5178

South Asian (SAS) AF: 0.864 AC: 4168 AN: 4826

European-Finnish (FIN) AF: 0.933 AC: 9895 AN: 10604

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.862 AC: 58626 AN: 68006

Other (OTH) AF: 0.857 AC: 1809 AN: 2110

Alfa AF: 0.863 Hom.: 97012

Bravo AF: 0.860

Asia WGS AF: 0.912 AC: 3168 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.16
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4672448; hg19: chr2-61928100;