rs6446693

Variant names:

• chr4-4853353-C-T
• rs6446693

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 0.578 in 151,934 control chromosomes in the GnomAD database, including 26,812 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 0.58 (26812 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.35
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 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: 0.578 AC: 87744 AN: 151818 Hom.: 26765 Cov.: 32

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.578 AC: 87843 AN: 151934 Hom.: 26812 Cov.: 32 AF XY: 0.580 AC XY: 43110 AN XY: 74274

African (AFR) AF: 0.786 AC: 32585 AN: 41432

American (AMR) AF: 0.609 AC: 9297 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1679 AN: 3466

East Asian (EAS) AF: 0.392 AC: 2024 AN: 5160

South Asian (SAS) AF: 0.589 AC: 2839 AN: 4816

European-Finnish (FIN) AF: 0.509 AC: 5363 AN: 10538

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32538 AN: 67944

Other (OTH) AF: 0.524 AC: 1104 AN: 2108

Alfa AF: 0.507 Hom.: 16470

Bravo AF: 0.591

Asia WGS AF: 0.496 AC: 1728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.0060
DANN	Benign	0.81
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs6446693; hg19: chr4-4855080;