chr6-36548590-T-C

Variant names:

• chr6-36548590-T-C
• rs1744659

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 0.254 in 151,912 control chromosomes in the GnomAD database, including 6,947 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 0.25 (6947 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 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: 0.254 AC: 38556 AN: 151794 Hom.: 6907 Cov.: 31

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.254 AC: 38648 AN: 151912 Hom.: 6947 Cov.: 31 AF XY: 0.254 AC XY: 18853 AN XY: 74260

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.234

Alfa AF: 0.205 Hom.: 601

Bravo AF: 0.285

Asia WGS AF: 0.193 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1744659; hg19: chr6-36516367;