rs261097

Variant names:

• chr5-102123983-T-G
• rs261097

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 0.215 in 151,840 control chromosomes in the GnomAD database, including 3,989 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 0.21 (3989 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.423

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 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: 0.215 AC: 32622 AN: 151722 Hom.: 3988 Cov.: 32

Gnomad AFR AF: 0.0981

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.215 AC: 32609 AN: 151840 Hom.: 3989 Cov.: 32 AF XY: 0.215 AC XY: 15920 AN XY: 74216

Gnomad4 AFR AF: 0.0979

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.222

Alfa AF: 0.250 Hom.: 621

Bravo AF: 0.210

Asia WGS AF: 0.193 AC: 669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs261097; hg19: chr5-101459687;