chr6-88473861-G-A

Position:

• chr6-88473861-G-A

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 0.0411 in 152,144 control chromosomes in the GnomAD database, including 140 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 0.041 (140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0411 AC: 6251 AN: 152026 Hom.: 140 Cov.: 32

Gnomad AFR AF: 0.0205

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.0438

Gnomad ASJ AF: 0.0894

Gnomad EAS AF: 0.0206

Gnomad SAS AF: 0.0664

Gnomad FIN AF: 0.0613

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0468

Gnomad OTH AF: 0.0468

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

GnomAD4 genome AF: 0.0411 AC: 6250 AN: 152144 Hom.: 140 Cov.: 32 AF XY: 0.0424 AC XY: 3152 AN XY: 74384

Gnomad4 AFR AF: 0.0205

Gnomad4 AMR AF: 0.0436

Gnomad4 ASJ AF: 0.0894

Gnomad4 EAS AF: 0.0209

Gnomad4 SAS AF: 0.0660

Gnomad4 FIN AF: 0.0613

Gnomad4 NFE AF: 0.0468

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0473 Hom.: 64

Bravo AF: 0.0395

Asia WGS AF: 0.0600 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	15
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11757661; hg19: chr6-89183580;