chr7-38634233-A-G

Variant names:

• chr7-38634233-A-G
• rs9918553

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 0.32 in 152,120 control chromosomes in the GnomAD database, including 8,563 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 0.32 (8563 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 4 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 = 0.449 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: 0.320 AC: 48612 AN: 152002 Hom.: 8539 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.320 AC: 48674 AN: 152120 Hom.: 8563 Cov.: 32 AF XY: 0.325 AC XY: 24163 AN XY: 74376

African (AFR) AF: 0.455 AC: 18860 AN: 41484

American (AMR) AF: 0.257 AC: 3925 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3472

East Asian (EAS) AF: 0.366 AC: 1898 AN: 5186

South Asian (SAS) AF: 0.404 AC: 1946 AN: 4818

European-Finnish (FIN) AF: 0.353 AC: 3737 AN: 10572

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16297 AN: 67986

Other (OTH) AF: 0.290 AC: 612 AN: 2110

Alfa AF: 0.267 Hom.: 10757

Bravo AF: 0.321

Asia WGS AF: 0.382 AC: 1327 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	1.5
DANN	Benign	0.86
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs9918553; hg19: chr7-38673833;