7-150715229-C-T

Variant names:

• chr7-150715229-C-T
• rs10488372

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 0.323 in 151,940 control chromosomes in the GnomAD database, including 8,077 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 0.32 (8077 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 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: 0.322 AC: 48931 AN: 151822 Hom.: 8059 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.323 AC: 49001 AN: 151940 Hom.: 8077 Cov.: 31 AF XY: 0.326 AC XY: 24189 AN XY: 74244

African (AFR) AF: 0.302 AC: 12501 AN: 41434

American (AMR) AF: 0.324 AC: 4948 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1243 AN: 3470

East Asian (EAS) AF: 0.487 AC: 2512 AN: 5158

South Asian (SAS) AF: 0.303 AC: 1460 AN: 4818

European-Finnish (FIN) AF: 0.352 AC: 3707 AN: 10528

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21535 AN: 67944

Other (OTH) AF: 0.338 AC: 713 AN: 2112

Alfa AF: 0.320 Hom.: 19549

Bravo AF: 0.320

Asia WGS AF: 0.379 AC: 1317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.72
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs10488372; hg19: chr7-150412317;