7-87492706-G-T

Variant names:

• chr7-87492706-G-T
• rs2178658

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 0.242 in 152,098 control chromosomes in the GnomAD database, including 4,784 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 0.24 (4784 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.333 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: 0.242 AC: 36771 AN: 151980 Hom.: 4774 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.242 AC: 36792 AN: 152098 Hom.: 4784 Cov.: 32 AF XY: 0.240 AC XY: 17875 AN XY: 74352

African (AFR) AF: 0.164 AC: 6793 AN: 41508

American (AMR) AF: 0.330 AC: 5034 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1357 AN: 3468

East Asian (EAS) AF: 0.346 AC: 1788 AN: 5164

South Asian (SAS) AF: 0.237 AC: 1143 AN: 4818

European-Finnish (FIN) AF: 0.162 AC: 1710 AN: 10574

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18101 AN: 67976

Other (OTH) AF: 0.286 AC: 604 AN: 2112

Alfa AF: 0.263 Hom.: 12016

Bravo AF: 0.255

Asia WGS AF: 0.281 AC: 976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.33
PhyloP100		0.037

Splicing

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

Other links and lift over

dbSNP: rs2178658; hg19: chr7-87122022;