rs1468375

Variant names:

• chr7-145337519-C-A
• rs1468375

Your query was ambiguous. Multiple possible variants found:

• chr7-145337519-C-A
• chr7-145337519-C-T

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 0.402 in 151,914 control chromosomes in the GnomAD database, including 12,782 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 0.40 (12782 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.894
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.454 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: 0.402 AC: 61002 AN: 151796 Hom.: 12774 Cov.: 31

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.402 AC: 61047 AN: 151914 Hom.: 12782 Cov.: 31 AF XY: 0.399 AC XY: 29588 AN XY: 74214

African (AFR) AF: 0.300 AC: 12439 AN: 41444

American (AMR) AF: 0.460 AC: 7019 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1827 AN: 3466

East Asian (EAS) AF: 0.204 AC: 1052 AN: 5152

South Asian (SAS) AF: 0.363 AC: 1739 AN: 4788

European-Finnish (FIN) AF: 0.416 AC: 4396 AN: 10560

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31155 AN: 67932

Other (OTH) AF: 0.429 AC: 906 AN: 2110

Alfa AF: 0.419 Hom.: 8492

Bravo AF: 0.397

Asia WGS AF: 0.260 AC: 902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.63
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs1468375; hg19: chr7-145034612;