chr6-41320065-T-C

Variant names:

• chr6-41320065-T-C
• rs612399

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 0.338 in 152,178 control chromosomes in the GnomAD database, including 9,099 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 0.34 (9099 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.466 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: 0.338 AC: 51454 AN: 152058 Hom.: 9090 Cov.: 33

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.338 AC: 51495 AN: 152178 Hom.: 9099 Cov.: 33 AF XY: 0.340 AC XY: 25291 AN XY: 74412

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.318

Alfa AF: 0.366 Hom.: 17261

Bravo AF: 0.323

Asia WGS AF: 0.495 AC: 1723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.5
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs612399; hg19: chr6-41287803;