rs1388240

Variant names:

• chr4-126736287-C-A
• rs1388240

Your query was ambiguous. Multiple possible variants found:

• chr4-126736287-C-A
• chr4-126736287-C-G
• chr4-126736287-C-T

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 0.319 in 151,952 control chromosomes in the GnomAD database, including 7,974 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 (7974 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 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: 0.319 AC: 48453 AN: 151834 Hom.: 7971 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.319 AC: 48466 AN: 151952 Hom.: 7974 Cov.: 32 AF XY: 0.322 AC XY: 23934 AN XY: 74254

African (AFR) AF: 0.267 AC: 11086 AN: 41458

American (AMR) AF: 0.280 AC: 4272 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1282 AN: 3466

East Asian (EAS) AF: 0.465 AC: 2398 AN: 5158

South Asian (SAS) AF: 0.382 AC: 1845 AN: 4824

European-Finnish (FIN) AF: 0.412 AC: 4337 AN: 10530

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.327 AC: 22199 AN: 67938

Other (OTH) AF: 0.325 AC: 688 AN: 2114

Alfa AF: 0.322 Hom.: 24625

Bravo AF: 0.306

Asia WGS AF: 0.414 AC: 1434 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.6
DANN	Benign	0.59
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1388240; hg19: chr4-127657442;