chr9-78936744-G-A

Variant names:

• chr9-78936744-G-A
• rs10512077

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 0.471 in 151,746 control chromosomes in the GnomAD database, including 18,229 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 0.47 (18229 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 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: 0.471 AC: 71377 AN: 151628 Hom.: 18191 Cov.: 31

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.471 AC: 71468 AN: 151746 Hom.: 18229 Cov.: 31 AF XY: 0.465 AC XY: 34480 AN XY: 74160

African (AFR) AF: 0.678 AC: 28076 AN: 41386

American (AMR) AF: 0.406 AC: 6185 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1656 AN: 3460

East Asian (EAS) AF: 0.259 AC: 1325 AN: 5110

South Asian (SAS) AF: 0.464 AC: 2232 AN: 4812

European-Finnish (FIN) AF: 0.343 AC: 3619 AN: 10540

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 26994 AN: 67908

Other (OTH) AF: 0.446 AC: 938 AN: 2102

Alfa AF: 0.229 Hom.: 438

Bravo AF: 0.481

Asia WGS AF: 0.370 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.66
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs10512077; hg19: chr9-81551660;