rs9397673

Variant names:

• chr6-153945574-A-G
• rs9397673

Your query was ambiguous. Multiple possible variants found:

• chr6-153945574-A-G
• chr6-153945574-A-T

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 0.236 in 152,126 control chromosomes in the GnomAD database, including 4,562 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 0.24 (4562 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.395
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.39 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: 0.236 AC: 35845 AN: 152006 Hom.: 4551 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.236 AC: 35862 AN: 152126 Hom.: 4562 Cov.: 32 AF XY: 0.244 AC XY: 18178 AN XY: 74364

African (AFR) AF: 0.177 AC: 7355 AN: 41508

American (AMR) AF: 0.398 AC: 6084 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 927 AN: 3472

East Asian (EAS) AF: 0.330 AC: 1706 AN: 5168

South Asian (SAS) AF: 0.390 AC: 1881 AN: 4818

European-Finnish (FIN) AF: 0.244 AC: 2580 AN: 10580

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14457 AN: 67982

Other (OTH) AF: 0.268 AC: 566 AN: 2114

Alfa AF: 0.224 Hom.: 12825

Bravo AF: 0.239

Asia WGS AF: 0.379 AC: 1319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.8
DANN	Benign	0.67
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs9397673; hg19: chr6-154266709;