rs1379996

Variant names:

• chr4-179740174-C-T
• rs1379996

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;