rs9498069

Variant names:

• chr6-148614507-T-A
• rs9498069

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 0.0573 in 152,220 control chromosomes in the GnomAD database, including 307 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 0.057 (307 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.142 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: 0.0573 AC: 8715 AN: 152104 Hom.: 306 Cov.: 32

Gnomad AFR AF: 0.0796

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.0312

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.0853

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0373

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0573 AC: 8728 AN: 152220 Hom.: 307 Cov.: 32 AF XY: 0.0603 AC XY: 4485 AN XY: 74424

African (AFR) AF: 0.0797 AC: 3307 AN: 41516

American (AMR) AF: 0.0311 AC: 476 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0412 AC: 143 AN: 3468

East Asian (EAS) AF: 0.151 AC: 782 AN: 5184

South Asian (SAS) AF: 0.0787 AC: 379 AN: 4818

European-Finnish (FIN) AF: 0.0853 AC: 904 AN: 10602

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0373 AC: 2536 AN: 68022

Other (OTH) AF: 0.0445 AC: 94 AN: 2112

Alfa AF: 0.0451 Hom.: 16

Bravo AF: 0.0535

Asia WGS AF: 0.106 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.66
PhyloP100		-0.031

Splicing

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

Other links and lift over

dbSNP: rs9498069; hg19: chr6-148935643;