4-90102161-C-T

Position:

• chr4-90102161-C-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 0.308 in 151,438 control chromosomes in the GnomAD database, including 8,247 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 0.31 (8247 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 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: 0.308 AC: 46624 AN: 151318 Hom.: 8250 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.308 AC: 46620 AN: 151438 Hom.: 8247 Cov.: 32 AF XY: 0.308 AC XY: 22773 AN XY: 73958

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.285

Alfa AF: 0.372 Hom.: 2340

Bravo AF: 0.288

Asia WGS AF: 0.232 AC: 797 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.82
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1838227; hg19: chr4-91023312;