rs6971109

Variant names:

• chr7-21183171-C-T
• rs6971109

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 0.259 in 151,750 control chromosomes in the GnomAD database, including 5,564 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 (5564 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 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: 0.259 AC: 39214 AN: 151632 Hom.: 5552 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.259 AC: 39264 AN: 151750 Hom.: 5564 Cov.: 32 AF XY: 0.254 AC XY: 18844 AN XY: 74134

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.246

Alfa AF: 0.222 Hom.: 6284

Bravo AF: 0.263

Asia WGS AF: 0.243 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6971109; hg19: chr7-21222790;