6-108010090-A-T

Variant names:

• chr6-108010090-A-T
• rs4946888

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 0.397 in 152,066 control chromosomes in the GnomAD database, including 17,409 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 0.40 (17409 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 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: 0.397 AC: 60313 AN: 151946 Hom.: 17349 Cov.: 32

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.397 AC: 60438 AN: 152066 Hom.: 17409 Cov.: 32 AF XY: 0.396 AC XY: 29460 AN XY: 74338

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.342

Alfa AF: 0.149 Hom.: 275

Bravo AF: 0.423

Asia WGS AF: 0.366 AC: 1273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.4
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4946888; hg19: chr6-108331294; COSMIC: COSV68860252;