4-99633245-G-T

Variant names:

• chr4-99633245-G-T
• rs7659550

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 0.463 in 152,184 control chromosomes in the GnomAD database, including 18,190 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 0.46 (18190 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 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: 0.463 AC: 70373 AN: 152066 Hom.: 18157 Cov.: 33

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.463 AC: 70447 AN: 152184 Hom.: 18190 Cov.: 33 AF XY: 0.456 AC XY: 33948 AN XY: 74422

African (AFR) AF: 0.669 AC: 27802 AN: 41532

American (AMR) AF: 0.382 AC: 5841 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2086 AN: 3470

East Asian (EAS) AF: 0.628 AC: 3255 AN: 5182

South Asian (SAS) AF: 0.425 AC: 2049 AN: 4816

European-Finnish (FIN) AF: 0.220 AC: 2333 AN: 10596

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25470 AN: 67968

Other (OTH) AF: 0.468 AC: 988 AN: 2112

Alfa AF: 0.403 Hom.: 21324

Bravo AF: 0.484

Asia WGS AF: 0.453 AC: 1576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.35
DANN	Benign	0.30
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs7659550; hg19: chr4-100554402;