rs2741335

Positions:

• chr8-27480274-A-C
• chr8-27480274-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 0.395 in 152,052 control chromosomes in the GnomAD database, including 14,613 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 0.39 (14613 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 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: 0.395 AC: 59949 AN: 151934 Hom.: 14581 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.395 AC: 60032 AN: 152052 Hom.: 14613 Cov.: 32 AF XY: 0.393 AC XY: 29235 AN XY: 74340

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.350

Alfa AF: 0.279 Hom.: 12959

Bravo AF: 0.402

Asia WGS AF: 0.268 AC: 933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.10
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2741335; hg19: chr8-27337791;