rs7665350

Variant names:

• chr4-102193865-G-A
• rs7665350

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 0.237 in 152,134 control chromosomes in the GnomAD database, including 5,057 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 0.24 (5057 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 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: 0.237 AC: 36055 AN: 152016 Hom.: 5035 Cov.: 33

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.237 AC: 36123 AN: 152134 Hom.: 5057 Cov.: 33 AF XY: 0.236 AC XY: 17568 AN XY: 74364

African (AFR) AF: 0.396 AC: 16434 AN: 41488

American (AMR) AF: 0.171 AC: 2617 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 401 AN: 3470

East Asian (EAS) AF: 0.197 AC: 1018 AN: 5180

South Asian (SAS) AF: 0.210 AC: 1012 AN: 4824

European-Finnish (FIN) AF: 0.199 AC: 2102 AN: 10564

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.173 AC: 11759 AN: 68002

Other (OTH) AF: 0.202 AC: 426 AN: 2114

Alfa AF: 0.192 Hom.: 13367

Bravo AF: 0.243

Asia WGS AF: 0.247 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.47
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs7665350; hg19: chr4-103115022;