rs4240580

Positions:

• chr6-99753590-A-G
• chr6-99753590-A-T

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.612

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.99753590A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0546

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.196

Alfa AF: 0.128 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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4240580; hg19: chr6-100201466;