rs1614309

chr6-29778107-G-Achr6-29778107-G-Cchr6-29778107-G-T

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 0.345 in 152,082 control chromosomes in the GnomAD database, including 9,529 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 0.35 (9529 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

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 (AFR) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52461 AN: 151964 Hom.: 9521 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.345 AC: 52491 AN: 152082 Hom.: 9529 Cov.: 32 AF XY: 0.339 AC XY: 25189 AN XY: 74342

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.349

Alfa AF: 0.330 Hom.: 3382

Bravo AF: 0.361

Asia WGS AF: 0.257 AC: 896 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	2.4
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: rs1614309; hg19: chr6-29745884;