rs6446700

Variant names:

• chr4-4909915-A-G
• rs6446700

Your query was ambiguous. Multiple possible variants found:

• chr4-4909915-A-G
• chr4-4909915-A-T

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 0.465 in 152,134 control chromosomes in the GnomAD database, including 16,798 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 0.46 (16798 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.81
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 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: 0.465 AC: 70632 AN: 152016 Hom.: 16777 Cov.: 33

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.465 AC: 70705 AN: 152134 Hom.: 16798 Cov.: 33 AF XY: 0.470 AC XY: 34942 AN XY: 74380

African (AFR) AF: 0.382 AC: 15844 AN: 41494

American (AMR) AF: 0.533 AC: 8142 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1370 AN: 3468

East Asian (EAS) AF: 0.575 AC: 2971 AN: 5170

South Asian (SAS) AF: 0.374 AC: 1800 AN: 4818

European-Finnish (FIN) AF: 0.557 AC: 5897 AN: 10590

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33274 AN: 67990

Other (OTH) AF: 0.444 AC: 938 AN: 2112

Alfa AF: 0.473 Hom.: 51618

Bravo AF: 0.460

Asia WGS AF: 0.456 AC: 1590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.024
DANN	Benign	0.44
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs6446700; hg19: chr4-4911642;