rs7044203

Variant names:

• chr9-75700836-C-T
• rs7044203

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 0.197 in 152,026 control chromosomes in the GnomAD database, including 3,135 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 0.20 (3135 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.205 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: 0.197 AC: 29991 AN: 151908 Hom.: 3133 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.0624

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.197 AC: 30008 AN: 152026 Hom.: 3135 Cov.: 32 AF XY: 0.200 AC XY: 14831 AN XY: 74302

African (AFR) AF: 0.184 AC: 7617 AN: 41508

American (AMR) AF: 0.211 AC: 3221 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 639 AN: 3468

East Asian (EAS) AF: 0.0625 AC: 323 AN: 5164

South Asian (SAS) AF: 0.113 AC: 545 AN: 4820

European-Finnish (FIN) AF: 0.295 AC: 3102 AN: 10526

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14027 AN: 67960

Other (OTH) AF: 0.184 AC: 388 AN: 2110

Alfa AF: 0.200 Hom.: 12578

Bravo AF: 0.191

Asia WGS AF: 0.0790 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.70
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs7044203; hg19: chr9-78315752;