rs6837348

chr4-111787647-G-Achr4-111787647-G-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 0.289 in 152,064 control chromosomes in the GnomAD database, including 6,609 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 0.29 (6609 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.47

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 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: 0.290 AC: 44004 AN: 151946 Hom.: 6602 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.289 AC: 44019 AN: 152064 Hom.: 6609 Cov.: 32 AF XY: 0.292 AC XY: 21724 AN XY: 74330

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.274

Alfa AF: 0.295 Hom.: 1036

Bravo AF: 0.290

Asia WGS AF: 0.397 AC: 1377 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.0010
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6837348; hg19: chr4-112708803;