chr6-88473861-G-A

Variant names:

• chr6-88473861-G-A
• rs11757661

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;