7-86543860-C-T

Variant names:

• chr7-86543860-C-T
• rs1527769

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 0.0625 in 152,240 control chromosomes in the GnomAD database, including 395 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 0.062 (395 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0964 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: 0.0625 AC: 9514 AN: 152122 Hom.: 394 Cov.: 32

Gnomad AFR AF: 0.0165

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0335

Gnomad ASJ AF: 0.0567

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0216

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0984

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0625 AC: 9513 AN: 152240 Hom.: 395 Cov.: 32 AF XY: 0.0609 AC XY: 4530 AN XY: 74408

African (AFR) AF: 0.0164 AC: 682 AN: 41572

American (AMR) AF: 0.0334 AC: 510 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0567 AC: 197 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.0218 AC: 105 AN: 4820

European-Finnish (FIN) AF: 0.105 AC: 1109 AN: 10588

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0984 AC: 6690 AN: 68008

Other (OTH) AF: 0.0534 AC: 113 AN: 2116

Alfa AF: 0.0783 Hom.: 324

Bravo AF: 0.0557

Asia WGS AF: 0.0120 AC: 42 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	13
DANN	Benign	0.71
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1527769; hg19: chr7-86173176;