rs41401746

Positions:

• chr6-137219796-GAA-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.00478 in 967,358 control chromosomes in the GnomAD database, including 121 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.019 (77 hom., cov: 32)
  • Exomes 𝑓: 0.0021 (44 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0189 AC: 2881 AN: 152122 Hom.: 77 Cov.: 32

Gnomad AFR AF: 0.0629

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0116

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000573

Gnomad OTH AF: 0.0263

GnomAD4 exome AF: 0.00213 AC: 1739 AN: 815118 Hom.: 44 AF XY: 0.00201 AC XY: 757 AN XY: 377042

Gnomad4 AFR exome AF: 0.0692

Gnomad4 AMR exome AF: 0.00826

Gnomad4 ASJ exome AF: 0.000993

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000621

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000750

Gnomad4 OTH exome AF: 0.00334

GnomAD4 genome AF: 0.0190 AC: 2886 AN: 152240 Hom.: 77 Cov.: 32 AF XY: 0.0183 AC XY: 1360 AN XY: 74450

Gnomad4 AFR AF: 0.0628

Gnomad4 AMR AF: 0.0116

Gnomad4 ASJ AF: 0.00115

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000573

Gnomad4 OTH AF: 0.0260

Alfa AF: 0.0135 Hom.: 5

Bravo AF: 0.0221

Asia WGS AF: 0.00462 AC: 16 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41401746; hg19: chr6-137540933;