rs1996020

Positions:

• chr4-144590042-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 0.237 in 151,818 control chromosomes in the GnomAD database, including 5,127 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 0.24 (5127 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.363 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: 0.237 AC: 35943 AN: 151700 Hom.: 5118 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.237 AC: 35992 AN: 151818 Hom.: 5127 Cov.: 32 AF XY: 0.238 AC XY: 17677 AN XY: 74198

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.240

Alfa AF: 0.186 Hom.: 1435

Bravo AF: 0.254

Asia WGS AF: 0.388 AC: 1350 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	0.86
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1996020; hg19: chr4-145511194;