rs1472343

chr6-164384226-T-Achr6-164384226-T-Cchr6-164384226-T-G

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 0.443 in 151,886 control chromosomes in the GnomAD database, including 15,195 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 0.44 (15195 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280

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 (SAS) allele frequency at 95% confidence interval = 0.496 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: 0.443 AC: 67187 AN: 151770 Hom.: 15154 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.443 AC: 67280 AN: 151886 Hom.: 15195 Cov.: 32 AF XY: 0.441 AC XY: 32739 AN XY: 74222

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.513

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.438

Alfa AF: 0.262 Hom.: 570

Bravo AF: 0.455

Asia WGS AF: 0.551 AC: 1913 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	0.063
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1472343; hg19: chr6-164805259; COSMIC: COSV60300793;