4-102771986-G-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 0.579 in 151,916 control chromosomes in the GnomAD database, including 26,870 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 0.58 (26870 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 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: 0.579 AC: 87869 AN: 151798 Hom.: 26826 Cov.: 32

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.579 AC: 87968 AN: 151916 Hom.: 26870 Cov.: 32 AF XY: 0.578 AC XY: 42866 AN XY: 74222

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.583

Alfa AF: 0.528 Hom.: 2560

Bravo AF: 0.596

Asia WGS AF: 0.527 AC: 1829 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.7
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs223475; hg19: chr4-103693143;