rs7707803

Variant names:

• chr5-148008671-A-G
• rs7707803

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 0.153 in 152,212 control chromosomes in the GnomAD database, including 1,949 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 0.15 (1949 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.563
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 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: 0.153 AC: 23203 AN: 152092 Hom.: 1944 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.153 AC: 23231 AN: 152212 Hom.: 1949 Cov.: 32 AF XY: 0.151 AC XY: 11204 AN XY: 74434

African (AFR) AF: 0.144 AC: 5969 AN: 41540

American (AMR) AF: 0.171 AC: 2617 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0790 AC: 274 AN: 3468

East Asian (EAS) AF: 0.322 AC: 1661 AN: 5162

South Asian (SAS) AF: 0.186 AC: 897 AN: 4822

European-Finnish (FIN) AF: 0.112 AC: 1191 AN: 10610

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10121 AN: 68008

Other (OTH) AF: 0.160 AC: 337 AN: 2112

Alfa AF: 0.152 Hom.: 7964

Bravo AF: 0.160

Asia WGS AF: 0.278 AC: 965 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.3
DANN	Benign	0.65
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs7707803; hg19: chr5-147388234;