rs2505997

Positions:

• chr10-43074907-C-T

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 0.32 in 152,170 control chromosomes in the GnomAD database, including 7,955 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 0.32 (7955 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.365 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: 0.320 AC: 48633 AN: 152050 Hom.: 7927 Cov.: 33

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.320 AC: 48706 AN: 152170 Hom.: 7955 Cov.: 33 AF XY: 0.318 AC XY: 23649 AN XY: 74396

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.336

Alfa AF: 0.303 Hom.: 1011

Bravo AF: 0.335

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2505997; hg19: chr10-43570355;