rs7677253

Variant names:

• chr4-188923347-T-C
• rs7677253

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 0.0703 in 152,182 control chromosomes in the GnomAD database, including 440 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 0.070 (440 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0975 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: 0.0701 AC: 10662 AN: 152062 Hom.: 433 Cov.: 33

Gnomad AFR AF: 0.0995

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0545

Gnomad ASJ AF: 0.0669

Gnomad EAS AF: 0.0675

Gnomad SAS AF: 0.0840

Gnomad FIN AF: 0.0341

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0614

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0703 AC: 10696 AN: 152182 Hom.: 440 Cov.: 33 AF XY: 0.0706 AC XY: 5249 AN XY: 74400

African (AFR) AF: 0.100 AC: 4156 AN: 41528

American (AMR) AF: 0.0544 AC: 831 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0669 AC: 232 AN: 3470

East Asian (EAS) AF: 0.0675 AC: 349 AN: 5174

South Asian (SAS) AF: 0.0839 AC: 404 AN: 4818

European-Finnish (FIN) AF: 0.0341 AC: 361 AN: 10596

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0614 AC: 4177 AN: 67992

Other (OTH) AF: 0.0615 AC: 130 AN: 2114

Alfa AF: 0.0646 Hom.: 550

Bravo AF: 0.0725

Asia WGS AF: 0.0720 AC: 252 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	1.6
DANN	Benign	0.69
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7677253; hg19: chr4-189844501;