rs2527887

Variant names:

• chr7-99953331-T-A
• rs2527887

Your query was ambiguous. Multiple possible variants found:

• chr7-99953331-T-A
• chr7-99953331-T-C

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 0.359 in 152,052 control chromosomes in the GnomAD database, including 9,905 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 0.36 (9905 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.401 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: 0.359 AC: 54485 AN: 151934 Hom.: 9890 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.359 AC: 54530 AN: 152052 Hom.: 9905 Cov.: 32 AF XY: 0.359 AC XY: 26688 AN XY: 74344

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.349

Alfa AF: 0.236 Hom.: 529

Bravo AF: 0.343

Asia WGS AF: 0.369 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2527887; hg19: chr7-99550954;