4-67448722-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000250075 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000250075	ENST00000502400.5	n.34+19496T>C		intron_variant	Intron 1 of 3	2
ENSG00000250075	ENST00000652065.1	n.141+6737T>C		intron_variant	Intron 2 of 4

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

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.734

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.672

Alfa AF: 0.610 Hom.: 12750

Bravo AF: 0.646

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7681618; hg19: chr4-68314440;