rs41440

chr7-86145233-A-G

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 0.26 in 152,006 control chromosomes in the GnomAD database, including 5,555 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 0.26 (5555 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 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: 0.261 AC: 39587 AN: 151888 Hom.: 5554 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.260 AC: 39596 AN: 152006 Hom.: 5555 Cov.: 32 AF XY: 0.261 AC XY: 19353 AN XY: 74280

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.227

Alfa AF: 0.248 Hom.: 2223

Bravo AF: 0.251

Asia WGS AF: 0.137 AC: 477 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	3.3
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41440; hg19: chr7-85774549;