rs10487416

Variant names:

• chr7-120100989-T-C
• rs10487416

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 0.0514 in 152,190 control chromosomes in the GnomAD database, including 359 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 0.051 (359 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 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: 0.0514 AC: 7814 AN: 152072 Hom.: 358 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0325

Gnomad ASJ AF: 0.0398

Gnomad EAS AF: 0.0317

Gnomad SAS AF: 0.0428

Gnomad FIN AF: 0.0436

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0170

Gnomad OTH AF: 0.0450

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

GnomAD4 genome AF: 0.0514 AC: 7822 AN: 152190 Hom.: 359 Cov.: 32 AF XY: 0.0510 AC XY: 3794 AN XY: 74400

African (AFR) AF: 0.123 AC: 5098 AN: 41500

American (AMR) AF: 0.0325 AC: 496 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0398 AC: 138 AN: 3470

East Asian (EAS) AF: 0.0318 AC: 165 AN: 5186

South Asian (SAS) AF: 0.0426 AC: 206 AN: 4832

European-Finnish (FIN) AF: 0.0436 AC: 462 AN: 10606

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0169 AC: 1152 AN: 68004

Other (OTH) AF: 0.0445 AC: 94 AN: 2112

Alfa AF: 0.0462 Hom.: 36

Bravo AF: 0.0527

Asia WGS AF: 0.0410 AC: 143 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
DANN	Benign	0.58
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs10487416; hg19: chr7-119741043;