chr6-149121109-A-G

Variant names:

• chr6-149121109-A-G
• rs7761698

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 0.214 in 151,954 control chromosomes in the GnomAD database, including 3,757 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 (3757 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 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: 0.213 AC: 32397 AN: 151836 Hom.: 3750 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.214 AC: 32451 AN: 151954 Hom.: 3757 Cov.: 32 AF XY: 0.218 AC XY: 16174 AN XY: 74244

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.211

Alfa AF: 0.189 Hom.: 5558

Bravo AF: 0.199

Asia WGS AF: 0.252 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7761698; hg19: chr6-149442245;