9-78681003-T-C

Variant names:

• chr9-78681003-T-C
• rs722642

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 0.721 in 151,958 control chromosomes in the GnomAD database, including 39,913 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 0.72 (39913 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.57
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 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: 0.721 AC: 109416 AN: 151838 Hom.: 39869 Cov.: 31

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.721 AC: 109520 AN: 151958 Hom.: 39913 Cov.: 31 AF XY: 0.722 AC XY: 53652 AN XY: 74272

African (AFR) AF: 0.821 AC: 34020 AN: 41432

American (AMR) AF: 0.786 AC: 11997 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2395 AN: 3470

East Asian (EAS) AF: 0.674 AC: 3461 AN: 5136

South Asian (SAS) AF: 0.553 AC: 2660 AN: 4808

European-Finnish (FIN) AF: 0.727 AC: 7675 AN: 10552

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44905 AN: 67980

Other (OTH) AF: 0.733 AC: 1549 AN: 2114

Alfa AF: 0.702 Hom.: 13467

Bravo AF: 0.732

Asia WGS AF: 0.651 AC: 2258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.078
DANN	Benign	0.64
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs722642; hg19: chr9-81295919;