4-67448722-A-G

Variant names:

• chr4-67448722-A-G
• rs7681618
• ENST00000502400.5:n.34+19496T>C

Variant summary

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

The ENST00000502400.5(ENSG00000250075):​n.34+19496T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 151,922 control chromosomes in the GnomAD database, including 30,536 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 0.63 (30536 hom., cov: 32)
• Consequence: ENSG00000250075 ENST00000502400.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 1 publications found

Genes affected

ENSG00000250075 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502400.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250075	ENST00000502400.5	TSL:2	n.34+19496T>C		intron	N/A
	ENSG00000250075	ENST00000652065.1		n.141+6737T>C		intron	N/A
	ENSG00000250075	ENST00000783862.1		n.127+6737T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95818 AN: 151804 Hom.: 30493 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.631 AC: 95908 AN: 151922 Hom.: 30536 Cov.: 32 AF XY: 0.636 AC XY: 47241 AN XY: 74244

African (AFR) AF: 0.633 AC: 26245 AN: 41452

American (AMR) AF: 0.734 AC: 11209 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2187 AN: 3468

East Asian (EAS) AF: 0.813 AC: 4206 AN: 5172

South Asian (SAS) AF: 0.698 AC: 3367 AN: 4822

European-Finnish (FIN) AF: 0.569 AC: 6003 AN: 10556

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40558 AN: 67862

Other (OTH) AF: 0.672 AC: 1417 AN: 2108

Alfa AF: 0.610 Hom.: 14186

Bravo AF: 0.646

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.50
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7681618; hg19: chr4-68314440;