4-141240325-A-C

Position:

• chr4-141240325-A-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 0.271 in 152,146 control chromosomes in the GnomAD database, including 6,015 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 0.27 (6015 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

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 = 0.59 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: 0.271 AC: 41174 AN: 152028 Hom.: 6025 Cov.: 33

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.271 AC: 41180 AN: 152146 Hom.: 6015 Cov.: 33 AF XY: 0.272 AC XY: 20227 AN XY: 74372

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.279

Alfa AF: 0.254 Hom.: 2571

Bravo AF: 0.278

Asia WGS AF: 0.391 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17350440; hg19: chr4-142161479;