6-51310444-C-T

Variant names:

• chr6-51310444-C-T
• rs1327261

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.153 in 151,564 control chromosomes in the GnomAD database, including 3,365 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 0.15 (3365 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.687

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.15).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 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: 0.153 AC: 23214 AN: 151446 Hom.: 3359 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0938

Gnomad ASJ AF: 0.0817

Gnomad EAS AF: 0.0598

Gnomad SAS AF: 0.0825

Gnomad FIN AF: 0.0507

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0611

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.153 AC: 23251 AN: 151564 Hom.: 3365 Cov.: 32 AF XY: 0.150 AC XY: 11093 AN XY: 74050

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.0936

Gnomad4 ASJ AF: 0.0817

Gnomad4 EAS AF: 0.0597

Gnomad4 SAS AF: 0.0828

Gnomad4 FIN AF: 0.0507

Gnomad4 NFE AF: 0.0611

Gnomad4 OTH AF: 0.131

Alfa AF: 0.0658 Hom.: 268

Bravo AF: 0.166

Asia WGS AF: 0.0890 AC: 311 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.15
CADD	Uncertain	24
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1327261; hg19: chr6-51175242;