chr4-171212786-A-C

Position:

• chr4-171212786-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 0.841 in 152,174 control chromosomes in the GnomAD database, including 54,112 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 0.84 (54112 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127

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 = 0.91 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: 0.841 AC: 127821 AN: 152056 Hom.: 54072 Cov.: 33

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.841 AC: 127919 AN: 152174 Hom.: 54112 Cov.: 33 AF XY: 0.846 AC XY: 62956 AN XY: 74384

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.899

Gnomad4 ASJ AF: 0.872

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.855

Alfa AF: 0.855 Hom.: 25334

Bravo AF: 0.837

Asia WGS AF: 0.901 AC: 3133 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	5.8
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2332211; hg19: chr4-172133937;