rs1379996

Variant names:

• chr4-179740174-C-T
• rs1379996

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0379 AC: 1573 AN: 41530

American (AMR) AF: 0.00841 AC: 128 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3472

East Asian (EAS) AF: 0.150 AC: 777 AN: 5176

South Asian (SAS) AF: 0.0682 AC: 329 AN: 4824

European-Finnish (FIN) AF: 0.0360 AC: 381 AN: 10596

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0147 AC: 1002 AN: 67976

Other (OTH) AF: 0.0232 AC: 49 AN: 2112

Alfa AF: 0.0188 Hom.: 106

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1379996; hg19: chr4-180661327;