rs1331574

Variant names:

• chr6-115319548-A-G
• rs1331574

Your query was ambiguous. Multiple possible variants found:

• chr6-115319548-A-G
• chr6-115319548-A-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 0.257 in 151,976 control chromosomes in the GnomAD database, including 5,504 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 0.26 (5504 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.316 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: 0.257 AC: 38970 AN: 151858 Hom.: 5499 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.257 AC: 38987 AN: 151976 Hom.: 5504 Cov.: 32 AF XY: 0.254 AC XY: 18890 AN XY: 74266

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.272

Alfa AF: 0.276 Hom.: 2506

Bravo AF: 0.260

Asia WGS AF: 0.244 AC: 852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.43
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1331574; hg19: chr6-115640712; COSMIC: COSV50466786;