chr6-10230572-A-G

Position:

• chr6-10230572-A-G

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 0.901 in 152,052 control chromosomes in the GnomAD database, including 63,097 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 0.90 (63097 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.986 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.10230572A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.901 AC: 136858 AN: 151936 Hom.: 63060 Cov.: 31

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.944

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.983

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.921

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

GnomAD4 genome AF: 0.901 AC: 136944 AN: 152052 Hom.: 63097 Cov.: 31 AF XY: 0.904 AC XY: 67179 AN XY: 74348

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.944

Gnomad4 ASJ AF: 0.983

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.983

Gnomad4 FIN AF: 0.997

Gnomad4 NFE AF: 0.992

Gnomad4 OTH AF: 0.922

Alfa AF: 0.941 Hom.: 10013

Bravo AF: 0.887

Asia WGS AF: 0.960 AC: 3330 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6905649; hg19: chr6-10230805;