rs1416546

Variant names:

• chr6-72412204-A-G
• rs1416546

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.321 in 152,202 control chromosomes in the GnomAD database, including 8,403 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 0.32 (8403 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.749
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 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: 0.321 AC: 48820 AN: 152084 Hom.: 8401 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.321 AC: 48840 AN: 152202 Hom.: 8403 Cov.: 32 AF XY: 0.316 AC XY: 23559 AN XY: 74438

African (AFR) AF: 0.281 AC: 11666 AN: 41528

American (AMR) AF: 0.254 AC: 3887 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1378 AN: 3468

East Asian (EAS) AF: 0.0249 AC: 129 AN: 5184

South Asian (SAS) AF: 0.320 AC: 1544 AN: 4830

European-Finnish (FIN) AF: 0.304 AC: 3218 AN: 10592

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25752 AN: 67982

Other (OTH) AF: 0.325 AC: 687 AN: 2112

Alfa AF: 0.361 Hom.: 17364

Bravo AF: 0.315

Asia WGS AF: 0.203 AC: 708 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.2
DANN	Benign	0.52
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs1416546; hg19: chr6-73121906; COSMIC: COSV69405016;