rs7102273

Variant names:

• chr11-68618111-T-C
• rs7102273

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 0.257 in 152,168 control chromosomes in the GnomAD database, including 5,290 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 0.26 (5290 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.97

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 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: 0.257 AC: 39133 AN: 152050 Hom.: 5287 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.257 AC: 39157 AN: 152168 Hom.: 5290 Cov.: 32 AF XY: 0.250 AC XY: 18583 AN XY: 74404

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.288

Alfa AF: 0.250 Hom.: 607

Bravo AF: 0.273

Asia WGS AF: 0.199 AC: 694 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	0.26
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7102273; hg19: chr11-68385579;