7-155862999-C-T

Variant names:

• chr7-155862999-C-T
• rs34044649

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 0.439 in 152,102 control chromosomes in the GnomAD database, including 16,428 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 0.44 (16428 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.65 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: 0.439 AC: 66745 AN: 151984 Hom.: 16415 Cov.: 33

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.439 AC: 66778 AN: 152102 Hom.: 16428 Cov.: 33 AF XY: 0.438 AC XY: 32549 AN XY: 74354

African (AFR) AF: 0.199 AC: 8261 AN: 41506

American (AMR) AF: 0.488 AC: 7464 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1445 AN: 3468

East Asian (EAS) AF: 0.669 AC: 3442 AN: 5146

South Asian (SAS) AF: 0.456 AC: 2193 AN: 4814

European-Finnish (FIN) AF: 0.507 AC: 5368 AN: 10584

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37056 AN: 67980

Other (OTH) AF: 0.448 AC: 947 AN: 2114

Alfa AF: 0.439 Hom.: 2314

Bravo AF: 0.425

Asia WGS AF: 0.549 AC: 1909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.048
DANN	Benign	0.48
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs34044649; hg19: chr7-155655693;