9-105663868-T-C

Variant names:

• chr9-105663868-T-C
• rs7874737

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 0.38 in 149,842 control chromosomes in the GnomAD database, including 11,155 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 0.38 (11155 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 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: 0.380 AC: 56837 AN: 149734 Hom.: 11145 Cov.: 27

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.380 AC: 56870 AN: 149842 Hom.: 11155 Cov.: 27 AF XY: 0.382 AC XY: 27889 AN XY: 72984

African (AFR) AF: 0.330 AC: 13405 AN: 40612

American (AMR) AF: 0.447 AC: 6698 AN: 15000

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1609 AN: 3460

East Asian (EAS) AF: 0.612 AC: 3076 AN: 5030

South Asian (SAS) AF: 0.339 AC: 1589 AN: 4684

European-Finnish (FIN) AF: 0.360 AC: 3646 AN: 10132

Middle Eastern (MID) AF: 0.483 AC: 139 AN: 288

European-Non Finnish (NFE) AF: 0.377 AC: 25497 AN: 67654

Other (OTH) AF: 0.424 AC: 879 AN: 2072

Alfa AF: 0.392 Hom.: 13992

Bravo AF: 0.387

Asia WGS AF: 0.443 AC: 1538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.0
DANN	Benign	0.74
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs7874737; hg19: chr9-108426149;