chr4-38323415-T-C

Position:

• chr4-38323415-T-C

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 0.149 in 152,242 control chromosomes in the GnomAD database, including 2,469 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 0.15 (2469 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.764

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22646 AN: 152124 Hom.: 2469 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.0263

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0675

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.149 AC: 22659 AN: 152242 Hom.: 2469 Cov.: 33 AF XY: 0.150 AC XY: 11142 AN XY: 74434

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.0263

Gnomad4 NFE AF: 0.0674

Gnomad4 OTH AF: 0.146

Alfa AF: 0.0861 Hom.: 1394

Bravo AF: 0.161

Asia WGS AF: 0.194 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.8
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6856616; hg19: chr4-38325036;