7-150534221-C-T

Variant names:

• chr7-150534221-C-T
• rs11769828

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 0.19 in 152,190 control chromosomes in the GnomAD database, including 3,515 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 0.19 (3515 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.259 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: 0.190 AC: 28956 AN: 152072 Hom.: 3517 Cov.: 33

Gnomad AFR AF: 0.0449

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.190 AC: 28951 AN: 152190 Hom.: 3515 Cov.: 33 AF XY: 0.197 AC XY: 14627 AN XY: 74388

African (AFR) AF: 0.0448 AC: 1863 AN: 41550

American (AMR) AF: 0.266 AC: 4070 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3470

East Asian (EAS) AF: 0.176 AC: 907 AN: 5168

South Asian (SAS) AF: 0.234 AC: 1129 AN: 4818

European-Finnish (FIN) AF: 0.338 AC: 3573 AN: 10578

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15801 AN: 68000

Other (OTH) AF: 0.171 AC: 360 AN: 2110

Alfa AF: 0.161 Hom.: 458

Bravo AF: 0.180

Asia WGS AF: 0.205 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.3
DANN	Benign	0.30
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs11769828; hg19: chr7-150231309; COSMIC: COSV61540363;