rs41401746

Variant names:

• chr6-137219796-GAA-G
• rs41401746

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;