rs561332

Positions:

• chr6-11610348-C-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 0.284 in 152,008 control chromosomes in the GnomAD database, including 6,619 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 0.28 (6619 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.11610348C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43121 AN: 151890 Hom.: 6607 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.284 AC: 43171 AN: 152008 Hom.: 6619 Cov.: 32 AF XY: 0.289 AC XY: 21465 AN XY: 74284

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.300

Alfa AF: 0.230 Hom.: 6879

Bravo AF: 0.303

Asia WGS AF: 0.298 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs561332; hg19: chr6-11610581;