rs1937780

Variant names:

• chr6-38706674-G-A
• rs1937780

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;