4-11119136-T-C

Position:

• chr4-11119136-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 0.254 in 152,012 control chromosomes in the GnomAD database, including 5,168 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 0.25 (5168 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.311

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 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: 0.254 AC: 38538 AN: 151894 Hom.: 5160 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.254 AC: 38574 AN: 152012 Hom.: 5168 Cov.: 32 AF XY: 0.260 AC XY: 19313 AN XY: 74302

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.250

Alfa AF: 0.239 Hom.: 925

Bravo AF: 0.262

Asia WGS AF: 0.336 AC: 1164 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.1
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7662694; hg19: chr4-11120760;