9-10648555-A-T

Variant names:

• chr9-10648555-A-T
• rs10511550

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 0.218 in 152,102 control chromosomes in the GnomAD database, including 6,071 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 0.22 (6071 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.485 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: 0.218 AC: 33080 AN: 151984 Hom.: 6052 Cov.: 32

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0975

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.0898

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0848

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.218 AC: 33140 AN: 152102 Hom.: 6071 Cov.: 32 AF XY: 0.219 AC XY: 16295 AN XY: 74386

African (AFR) AF: 0.491 AC: 20327 AN: 41410

American (AMR) AF: 0.128 AC: 1957 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0975 AC: 338 AN: 3466

East Asian (EAS) AF: 0.336 AC: 1741 AN: 5178

South Asian (SAS) AF: 0.331 AC: 1598 AN: 4826

European-Finnish (FIN) AF: 0.0898 AC: 953 AN: 10614

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0848 AC: 5766 AN: 67990

Other (OTH) AF: 0.181 AC: 382 AN: 2112

Alfa AF: 0.155 Hom.: 444

Bravo AF: 0.227

Asia WGS AF: 0.300 AC: 1040 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.69
PhyloP100		-0.047

Splicing

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

Other links and lift over

dbSNP: rs10511550; hg19: chr9-10648555;