rs288944

Variant names:

• chr6-156565521-C-T
• rs288944

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 0.204 in 152,124 control chromosomes in the GnomAD database, including 3,242 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 0.20 (3242 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 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: 0.204 AC: 30942 AN: 152006 Hom.: 3235 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.0922

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.204 AC: 30973 AN: 152124 Hom.: 3242 Cov.: 32 AF XY: 0.204 AC XY: 15193 AN XY: 74352

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.0924

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.193

Alfa AF: 0.204 Hom.: 1644

Bravo AF: 0.198

Asia WGS AF: 0.190 AC: 659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs288944; hg19: chr6-156886655;