rs261097

Variant names:

• chr5-102123983-T-G
• rs261097

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 0.215 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0979 AC: 4063 AN: 41506

American (AMR) AF: 0.233 AC: 3550 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 684 AN: 3464

East Asian (EAS) AF: 0.177 AC: 918 AN: 5176

South Asian (SAS) AF: 0.192 AC: 927 AN: 4820

European-Finnish (FIN) AF: 0.264 AC: 2794 AN: 10570

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18886 AN: 67756

Other (OTH) AF: 0.222 AC: 468 AN: 2108

Alfa AF: 0.244 Hom.: 626

Bravo AF: 0.210

Asia WGS AF: 0.193 AC: 669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.58
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs261097; hg19: chr5-101459687;