4-64201688-G-A

Position:

• chr4-64201688-G-A

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 0.291 in 141,540 control chromosomes in the GnomAD database, including 6,672 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 0.29 (6672 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.291 AC: 41189 AN: 141550 Hom.: 6671 Cov.: 24

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.291 AC: 41195 AN: 141540 Hom.: 6672 Cov.: 24 AF XY: 0.290 AC XY: 19838 AN XY: 68402

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.302

Alfa AF: 0.340 Hom.: 898

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.084

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6841405; hg19: chr4-65067406;