rs1997179

Variant names:

• chr4-122063478-T-C
• rs1997179

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;