4-67397481-A-T

Variant names:

• chr4-67397481-A-T
• rs11131698

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.941
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.275 AC: 11428 AN: 41484

American (AMR) AF: 0.218 AC: 3325 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 426 AN: 3466

East Asian (EAS) AF: 0.572 AC: 2945 AN: 5148

South Asian (SAS) AF: 0.307 AC: 1480 AN: 4814

European-Finnish (FIN) AF: 0.108 AC: 1146 AN: 10594

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0991 AC: 6740 AN: 68000

Other (OTH) AF: 0.203 AC: 428 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	11
DANN	Benign	0.61
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs11131698; hg19: chr4-68263199;