9-124100672-A-G

Variant names:

• chr9-124100672-A-G
• rs6478644

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 0.441 in 151,892 control chromosomes in the GnomAD database, including 14,902 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 0.44 (14902 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 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: 0.441 AC: 66971 AN: 151774 Hom.: 14879 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.441 AC: 67033 AN: 151892 Hom.: 14902 Cov.: 32 AF XY: 0.442 AC XY: 32802 AN XY: 74218

African (AFR) AF: 0.475 AC: 19661 AN: 41388

American (AMR) AF: 0.515 AC: 7866 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1387 AN: 3470

East Asian (EAS) AF: 0.523 AC: 2699 AN: 5156

South Asian (SAS) AF: 0.353 AC: 1701 AN: 4814

European-Finnish (FIN) AF: 0.440 AC: 4634 AN: 10536

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27630 AN: 67934

Other (OTH) AF: 0.430 AC: 908 AN: 2110

Alfa AF: 0.409 Hom.: 20386

Bravo AF: 0.454

Asia WGS AF: 0.406 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.46
DANN	Benign	0.52
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6478644; hg19: chr9-126862951;