7-89348607-T-C

Variant names:

• chr7-89348607-T-C
• rs10487076

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 0.0422 in 152,246 control chromosomes in the GnomAD database, including 778 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 0.042 (778 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) 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: 0.0422 AC: 6421 AN: 152126 Hom.: 777 Cov.: 32

Gnomad AFR AF: 0.0194

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0133

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00607

Gnomad OTH AF: 0.0430

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

GnomAD4 genome AF: 0.0422 AC: 6426 AN: 152246 Hom.: 778 Cov.: 32 AF XY: 0.0475 AC XY: 3534 AN XY: 74442

African (AFR) AF: 0.0193 AC: 804 AN: 41568

American (AMR) AF: 0.112 AC: 1706 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0112 AC: 39 AN: 3470

East Asian (EAS) AF: 0.470 AC: 2426 AN: 5164

South Asian (SAS) AF: 0.165 AC: 796 AN: 4826

European-Finnish (FIN) AF: 0.0133 AC: 141 AN: 10622

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00607 AC: 413 AN: 68004

Other (OTH) AF: 0.0454 AC: 96 AN: 2114

Alfa AF: 0.0211 Hom.: 26

Bravo AF: 0.0514

Asia WGS AF: 0.308 AC: 1068 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.85
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs10487076; hg19: chr7-88977921;