rs1997179

Positions:

• chr4-122063478-T-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 0.2 in 152,120 control chromosomes in the GnomAD database, including 4,137 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 0.20 (4137 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 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: 0.200 AC: 30337 AN: 152002 Hom.: 4138 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0371

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0966

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.200 AC: 30360 AN: 152120 Hom.: 4137 Cov.: 32 AF XY: 0.193 AC XY: 14384 AN XY: 74372

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.0366

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0966

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.180

Alfa AF: 0.156 Hom.: 1015

Bravo AF: 0.208

Asia WGS AF: 0.107 AC: 372 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1997179; hg19: chr4-122984633;