6-10230572-A-G

Variant names:

• chr6-10230572-A-G
• rs6905649

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 0.901 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.681 AC: 28216 AN: 41442

American (AMR) AF: 0.944 AC: 14421 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.983 AC: 3411 AN: 3470

East Asian (EAS) AF: 0.968 AC: 5005 AN: 5170

South Asian (SAS) AF: 0.983 AC: 4745 AN: 4828

European-Finnish (FIN) AF: 0.997 AC: 10517 AN: 10546

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.992 AC: 67487 AN: 67998

Other (OTH) AF: 0.922 AC: 1947 AN: 2112

Alfa AF: 0.932 Hom.: 10190

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
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs6905649; hg19: chr6-10230805;