rs2741354

Variant names:

• chr8-27557959-C-T
• rs2741354

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.581 in 151,974 control chromosomes in the GnomAD database, including 26,099 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 0.58 (26099 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.651 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: 0.582 AC: 88309 AN: 151856 Hom.: 26079 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.581 AC: 88372 AN: 151974 Hom.: 26099 Cov.: 32 AF XY: 0.581 AC XY: 43138 AN XY: 74278

African (AFR) AF: 0.494 AC: 20480 AN: 41438

American (AMR) AF: 0.661 AC: 10096 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2226 AN: 3468

East Asian (EAS) AF: 0.352 AC: 1816 AN: 5162

South Asian (SAS) AF: 0.574 AC: 2760 AN: 4806

European-Finnish (FIN) AF: 0.593 AC: 6260 AN: 10558

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.627 AC: 42605 AN: 67960

Other (OTH) AF: 0.578 AC: 1221 AN: 2112

Alfa AF: 0.615 Hom.: 21701

Bravo AF: 0.580

Asia WGS AF: 0.508 AC: 1764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.8
DANN	Benign	0.75
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2741354; hg19: chr8-27415476; COSMIC: COSV71824055;