7-96733032-G-T

Variant names:

• chr7-96733032-G-T
• rs1464807

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 0.0988 in 152,070 control chromosomes in the GnomAD database, including 798 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 0.099 (798 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 9 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 (EAS) allele frequency at 95% confidence interval = 0.142 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: 0.0989 AC: 15021 AN: 151952 Hom.: 798 Cov.: 31

Gnomad AFR AF: 0.0582

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.0988 AC: 15020 AN: 152070 Hom.: 798 Cov.: 31 AF XY: 0.101 AC XY: 7508 AN XY: 74318

African (AFR) AF: 0.0582 AC: 2415 AN: 41492

American (AMR) AF: 0.103 AC: 1567 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3472

East Asian (EAS) AF: 0.151 AC: 780 AN: 5164

South Asian (SAS) AF: 0.115 AC: 552 AN: 4816

European-Finnish (FIN) AF: 0.123 AC: 1295 AN: 10568

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7631 AN: 67968

Other (OTH) AF: 0.112 AC: 236 AN: 2114

Alfa AF: 0.105 Hom.: 1502

Bravo AF: 0.0963

Asia WGS AF: 0.140 AC: 486 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	0.76
DANN	Benign	0.48
PhyloP100		-0.062

Splicing

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

Other links and lift over

dbSNP: rs1464807; hg19: chr7-96362344;