rs1937780

chr6-38706674-G-A

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 0.279 in 152,112 control chromosomes in the GnomAD database, including 7,464 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 0.28 (7464 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.714

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42364 AN: 151994 Hom.: 7464 Cov.: 32

Gnomad AFR AF: 0.0811

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.0879

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.279 AC: 42365 AN: 152112 Hom.: 7464 Cov.: 32 AF XY: 0.276 AC XY: 20546 AN XY: 74348

Gnomad4 AFR AF: 0.0811

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.0882

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.290

Alfa AF: 0.358 Hom.: 4680

Bravo AF: 0.260

Asia WGS AF: 0.161 AC: 560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	8.0
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1937780; hg19: chr6-38674450;