4-67397481-A-T

Position:

• chr4-67397481-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.184 in 152,084 control chromosomes in the GnomAD database, including 3,587 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 0.18 (3587 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.941

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.67397481A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27997 AN: 151966 Hom.: 3565 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0991

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.184 AC: 28059 AN: 152084 Hom.: 3587 Cov.: 32 AF XY: 0.189 AC XY: 14051 AN XY: 74372

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.572

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.0991

Gnomad4 OTH AF: 0.203

Alfa AF: 0.141 Hom.: 248

Bravo AF: 0.199

Asia WGS AF: 0.471 AC: 1638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	11
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11131698; hg19: chr4-68263199;