chr6-88133671-A-G

Variant names:

• chr6-88133671-A-G
• rs10485171

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 0.429 in 151,986 control chromosomes in the GnomAD database, including 14,662 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 0.43 (14662 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 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: 0.429 AC: 65152 AN: 151868 Hom.: 14670 Cov.: 33

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.0847

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.429 AC: 65162 AN: 151986 Hom.: 14662 Cov.: 33 AF XY: 0.426 AC XY: 31632 AN XY: 74282

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.0847

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.381

Alfa AF: 0.426 Hom.: 28073

Bravo AF: 0.411

Asia WGS AF: 0.243 AC: 844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	8.3
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485171; hg19: chr6-88843390; COSMIC: COSV69412238;