chr3-196618278-A-C

Position:

• chr3-196618278-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 0.0997 in 152,128 control chromosomes in the GnomAD database, including 922 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 0.10 (922 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 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: 0.0997 AC: 15151 AN: 152010 Hom.: 910 Cov.: 32

Gnomad AFR AF: 0.0451

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0918

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0997 AC: 15171 AN: 152128 Hom.: 922 Cov.: 32 AF XY: 0.101 AC XY: 7492 AN XY: 74374

Gnomad4 AFR AF: 0.0450

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.0918

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.114

Alfa AF: 0.121 Hom.: 1536

Bravo AF: 0.0964

Asia WGS AF: 0.202 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7426655; hg19: chr3-196345149;