4-107383042-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.025 in 152,266 control chromosomes in the GnomAD database, including 40 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 0.025 (40 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.950

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.025 (3814/152266) while in subpopulation EAS AF= 0.0396 (205/5182). AF 95% confidence interval is 0.0351. There are 40 homozygotes in gnomad4. There are 1875 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 40 gene

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: 0.0251 AC: 3814 AN: 152148 Hom.: 40 Cov.: 32

Gnomad AFR AF: 0.0182

Gnomad AMI AF: 0.00991

Gnomad AMR AF: 0.0358

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.0395

Gnomad SAS AF: 0.0234

Gnomad FIN AF: 0.0137

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0280

Gnomad OTH AF: 0.0340

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

GnomAD4 genome AF: 0.0250 AC: 3814 AN: 152266 Hom.: 40 Cov.: 32 AF XY: 0.0252 AC XY: 1875 AN XY: 74450

Gnomad4 AFR AF: 0.0181

Gnomad4 AMR AF: 0.0358

Gnomad4 ASJ AF: 0.0159

Gnomad4 EAS AF: 0.0396

Gnomad4 SAS AF: 0.0240

Gnomad4 FIN AF: 0.0137

Gnomad4 NFE AF: 0.0279

Gnomad4 OTH AF: 0.0336

Alfa AF: 0.0298 Hom.: 9

Bravo AF: 0.0267

Asia WGS AF: 0.0340 AC: 121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.36
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7680468; hg19: chr4-108304199;