rs1379996

chr4-179740174-C-T

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 0.0281 in 152,116 control chromosomes in the GnomAD database, including 121 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 0.028 (121 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.141 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: 0.0280 AC: 4262 AN: 151998 Hom.: 121 Cov.: 32

Gnomad AFR AF: 0.0379

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.00842

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.0675

Gnomad FIN AF: 0.0360

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0147

Gnomad OTH AF: 0.0211

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

GnomAD4 genome AF: 0.0281 AC: 4271 AN: 152116 Hom.: 121 Cov.: 32 AF XY: 0.0301 AC XY: 2241 AN XY: 74360

Gnomad4 AFR AF: 0.0379

Gnomad4 AMR AF: 0.00841

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.0682

Gnomad4 FIN AF: 0.0360

Gnomad4 NFE AF: 0.0147

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0170 Hom.: 10

Bravo AF: 0.0260

Asia WGS AF: 0.119 AC: 414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.14
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1379996; hg19: chr4-180661327;