chr6-43790587-A-C

Variant names:

• chr6-43790587-A-C
• rs6899540

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 0.16 in 152,110 control chromosomes in the GnomAD database, including 2,094 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 0.16 (2094 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.199 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: 0.159 AC: 24232 AN: 151992 Hom.: 2084 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.0742

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.160 AC: 24273 AN: 152110 Hom.: 2094 Cov.: 32 AF XY: 0.154 AC XY: 11487 AN XY: 74370

African (AFR) AF: 0.202 AC: 8387 AN: 41472

American (AMR) AF: 0.114 AC: 1747 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 562 AN: 3466

East Asian (EAS) AF: 0.0740 AC: 382 AN: 5164

South Asian (SAS) AF: 0.112 AC: 538 AN: 4818

European-Finnish (FIN) AF: 0.127 AC: 1341 AN: 10590

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10835 AN: 67990

Other (OTH) AF: 0.156 AC: 330 AN: 2112

Alfa AF: 0.160 Hom.: 1271

Bravo AF: 0.160

Asia WGS AF: 0.121 AC: 419 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	1.8
DANN	Benign	0.56
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6899540; hg19: chr6-43758324;