rs4240580

Variant names:

• chr6-99753590-A-G
• rs4240580

Your query was ambiguous. Multiple possible variants found:

• chr6-99753590-A-G
• chr6-99753590-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 0.182 in 152,112 control chromosomes in the GnomAD database, including 3,060 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 0.18 (3060 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.612
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.243 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: 0.182 AC: 27718 AN: 151994 Hom.: 3057 Cov.: 32

Gnomad AFR AF: 0.0546

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.182 AC: 27720 AN: 152112 Hom.: 3060 Cov.: 32 AF XY: 0.187 AC XY: 13914 AN XY: 74350

African (AFR) AF: 0.0546 AC: 2269 AN: 41546

American (AMR) AF: 0.249 AC: 3806 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 793 AN: 3472

East Asian (EAS) AF: 0.208 AC: 1074 AN: 5174

South Asian (SAS) AF: 0.208 AC: 1005 AN: 4826

European-Finnish (FIN) AF: 0.271 AC: 2869 AN: 10568

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.225 AC: 15261 AN: 67952

Other (OTH) AF: 0.196 AC: 414 AN: 2110

Alfa AF: 0.125 Hom.: 306

Bravo AF: 0.179

Asia WGS AF: 0.181 AC: 623 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.9
DANN	Benign	0.71
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs4240580; hg19: chr6-100201466;