rs1397413

Variant names:

• chr4-178292452-T-A
• rs1397413

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 0.32 in 152,090 control chromosomes in the GnomAD database, including 8,211 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 0.32 (8211 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 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: 0.320 AC: 48691 AN: 151972 Hom.: 8203 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.320 AC: 48706 AN: 152090 Hom.: 8211 Cov.: 32 AF XY: 0.321 AC XY: 23878 AN XY: 74322

African (AFR) AF: 0.290 AC: 12034 AN: 41512

American (AMR) AF: 0.217 AC: 3310 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 991 AN: 3468

East Asian (EAS) AF: 0.139 AC: 717 AN: 5170

South Asian (SAS) AF: 0.422 AC: 2031 AN: 4816

European-Finnish (FIN) AF: 0.396 AC: 4178 AN: 10562

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24467 AN: 67990

Other (OTH) AF: 0.291 AC: 613 AN: 2110

Alfa AF: 0.344 Hom.: 1146

Bravo AF: 0.301

Asia WGS AF: 0.273 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.39
DANN	Benign	0.45
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1397413; hg19: chr4-179213606;