6-31350367-T-C

Variant names:

• chr6-31350367-T-C
• rs2523619

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 0.232 in 152,002 control chromosomes in the GnomAD database, including 4,341 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 0.23 (4341 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204

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 (SAS) allele frequency at 95% confidence interval = 0.294 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: 0.232 AC: 35280 AN: 151884 Hom.: 4339 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.232 AC: 35303 AN: 152002 Hom.: 4341 Cov.: 31 AF XY: 0.234 AC XY: 17410 AN XY: 74312

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.270

Alfa AF: 0.215 Hom.: 5035

Bravo AF: 0.243

Asia WGS AF: 0.227 AC: 791 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	8.7
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2523619; hg19: chr6-31318144;